BASB119 Polypeptide and Polynucleotide from Moraxella Catarrhalis

ABSTRACT

The invention provides BASB119 polypeptides and polynucleotides encoding BASB119 polypeptides and methods for producing such polypeptides by recombinant techniques. Also provided are diagnostic, prophylactic and therapeutic uses.

FIELD OF THE INVENTION

This invention relates to polynucleotides, (herein referred to as“BASB119 polynucleotide(s)”), polypeptides encoded by them (referred toherein as “BASB119” or “BASB119 polypeptide(s)”), recombinant materialsand methods for their production. In another aspect, the inventionrelates to methods for using such polypeptides and polynucleotides,including vaccines against bacterial infections. In a further aspect,the invention relates to diagnostic assays for detecting infection ofcertain pathogens.

BACKGROUND OF THE INVENTION

Moraxella catarrhalis (also named Branhamella catarrhalis) is a Gramnegative bacteria frequently isolated from the human upper respiratorytract. It is responsible for several pathologies the main ones beingotitis media in infants and children, and pneumonia in elderlies. It isalso responsible of sinusitis, nosocomial infections and less frequentlyof invasive diseases.

Otitis media is an important childhood disease both by the number ofcases and its potential sequelae. More than 3.5 millions cases arerecorded every year in the United States, and it is estimated that 80%of the children have experienced at least one episode of otitis beforereaching the age of 3 (Klein, J O (1994) Clin. Inf. Dis 19:823). Leftuntreated, or becoming chronic, this disease may lead to hearing lossesthat could be temporary (in the case of fluid accumulation in the middleear) or permanent (if the auditive nerve is damaged). In infants, suchhearing losses may be responsible for a delayed speech learning.

Three bacterial species are primarily isolated from the middle ear ofchildren with otitis media: Streptococcus pneumoniae, non typeableHaemophilus influenza (NTHi) and M. catarrhalis. They are present in 60to 90% of the cases. A review of recent studies shows that S. pneumoniaeand NTHi represent both about 30%, and M. catarrhalis about 15% of theotitis media cases (Murphy, T F (1996) Microbiol. Rev. 60:267). Otherbacteria could be isolated from the middle car (H. influenza type B, S.pyogenes etc) but at a much lower frequency (2% of the cases or less).

Epidemiological data indicate that, for the pathogens found in themiddle ear, the colonization of the upper respiratory tract is anabsolute prerequisite for the development of an otitis; other arehowever also required to lead to the disease (Dickinson, D P et al.(1988) J. Infect. Dis. 158:205, Faden, H L et al. (1991) Ann. Otorhinol.Laryngol. 100:612). These are important to trigger the migration of thebacteria into the middle ear via the Eustachian tubes, followed by theinitiation of an inflammatory process. These factors are unknown todate. It has been postulated that a transient anomaly of the immunesystem following a viral infection, for example, could cause aninability to control the colonization of the respiratory tract (Faden, HL et al (1994) J. Infect. Dis. 169:1312). An alternative explanation isthat the exposure to environmental factors allow a more importantcolonization of some children, who subsequently become susceptible tothe development of otitis media because of the sustained presence ofmiddle ear pathogens (Murphy, T F (1996) Microbiol. Rev. 60:267).

The immune response to M. catarrhalis is poorly characterized. Theanalysis of strains isolated sequentially from the nasopharynx of babiesfollowed from 0 to 2 years of age, indicates that they get and eliminatefrequently new strains. This indicates that an efficacious immuneresponse against this bacteria is mounted by the colonized children(Faden, H L et al (1994) J. Infect. Dis. 169:1312).

In most adults tested, bactericidal antibodies have been identified(Chapman, A J et al. (1985) J. Infect. Dis. 151:878). Strains of M.catarrhalis present variations in their capacity to resist serumbactericidal activity: in general, isolates from diseased individualsare more resistant than those who are simply colonized (Hol, C et al.(1993) Lancet 341:1281, Jordan, K L et al. (1990) Am. J. Med. 88 (suppl.5A):28S). Serum resistance could therfore be considered as a virulencefactor of the bacteria. An opsonizing activity has been observed in thesera of children recovering from otitis media.

The antigens targetted by these different immune responses in humanshave not been identified, with the exception of OMP B1, a 84 kDa proteinwhich expression is regulated by iron, and that is recognized by thesera of patients with pneumonia (Sethi, S, et al. (1995) Infect. Immun.63:1516), and of UspA1 and UspA2 (Chen D. et al. (1999), Infect. Immun.67:1310).

A few other membrane proteins present on the surface of M. catarrhalishave been characterized using biochemical method, or for their potentialimplication in the induction of a protective immunity (for review, seeMurphy, T F (1996) Microbiol. Rev. 60:267). In a mouse pneumonia model,the presence of antibodies raised against some of them (UspA, CopB)favors a faster clearance of the pulmonary infection. Anotherpolypeptide (OMP CD) is highly conserved among M. catarrhalis strains,and presents homologies with a porin of Pseudomonas aeruginosa, whichhas been demonstrated efficacious against this bacterium in animalmodels.

The frequency of Moraxella catarrhalis infections has risen dramaticallyin the past few decades. This has been attributed to the emergence ofmultiply antibiotic resistant strains and an increasing population ofpeople with weakened immune systems. It is no longer uncommon to isolateMoraxella catarrhalis strains that are resistant to some or all of thestandard antibiotics. This phenomenon has created an unmet medical needand demand for new anti-microbial agents, vaccines, drug screeningmethods, and diagnostic tests for this organism.

SUMMARY OF THE INVENTION

The present invention relates to BASB119, in particular BASB119polypeptides and BASB119 polynucleotides, recombinant materials andmethods for their production. In another aspect, the invention relatesto methods for using such polypeptides and polynucleotides, includingprevention and treatment of microbial diseases, amongst others. In afurther aspect, the invention relates to diagnostic assays for detectingdiseases associated with microbial infections and conditions associatedwith such infections, such as assays for detecting expression oractivity of BASB119 polynucleotides or polypeptides.

Various changes and modifications within the spirit and scope of thedisclosed invention will become readily apparent to those skilled in theart from reading the following descriptions and from reading the otherparts of the present disclosure.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows the alignment of the BASB119 polynucleotide sequences.

FIG. 2 shows the alignment of the BASB119 polypeptide sequences.

FIG. 3-A shows Coomassie stained SDS-polyacrylamide gel of purifiedBASB119.

FIG. 3-B shows Western Blotting of purified BASB119.

DESCRIPTION OF THE INVENTION

The invention relates to BASB119 polypeptides and polynucleotides asdescribed in greater detail below. In particular, the invention relatesto polypeptides and polynucleotides of BASB119 of Moraxella catarrhalis,which is related by amino acid sequence homology to none of the knownprotein sequences. It is predicted to be a lipoprotein because it has asignal sequence characteristic of lipoprotein. The invention relatesespecially to BASB119 having the nucleotide and amino acid sequences setout in SEQ ID NO:1 or 3 and SEQ ID NO:2 or 4 respectively. It isunderstood that sequences recited in the Sequence Listing below as “DNA”represent an exemplification of one embodiment of the invention, sincethose of ordinary skill will recognize that such sequences can beusefully employed in polynucleotides in general, includingribopolynucleotides.

Polypeptides

In one aspect of the invention there are provided polypeptides ofMoraxella catarrhalis referred to herein as “BASB119” and “BASB119polypeptides” as well as biologically, diagnostically, prophylactically,clinically or therapeutically useful variants thereof, and compositionscomprising the same.

The present invention further provides for:

(a) an isolated polypeptide which comprises an amino acid sequence whichhas at least 85% identity, preferably at least 90% identity, morepreferably at least 95% identity, most preferably at least 97-99% orexact identity, to that of SEQ ID NO:2 or 4;(b) a polypeptide encoded by an isolated polynucleotide comprising apolynucleotide sequence which has at least 85% identity, preferably atleast 90% identity, more preferably at least 95% identity, even morepreferably at least 97-99% or exact identity to SEQ ID NO:1 or 3 overthe entire length of SEQ ID NO:1 or 3 respectively; or(c) a polypeptide encoded by an isolated polynucleotide comprising apolynucleotide sequence encoding a polypeptide which has at least 85%identity, preferably at least 90% identity, more preferably at least 95%identity, even more preferably at least 97-99% or exact identity, to theamino acid sequence of SEQ ID NO:2 or 4.

The BASB119 polypeptides provided in SEQ ID NO:2 or 4 are the BASB119polypeptides from Moraxella catarrhalis strain Mc2931 (ATCC 43617).

The invention also provides an immunogenic fragment of a BASB119polypeptide, that is, a contiguous portion of the BASB119 polypeptidewhich has the same or substantially the same immunogenic activity as thepolypeptide comprising the amino acid sequence of SEQ ID NO:2 or 4; Thatis to say, the fragment (if necessary when coupled to a carrier) iscapable of raising an immune response which recognises the BASB119polypeptide. Such an immunogenic fragment may include, for example, theBASB119 polypeptide lacking an N-terminal leader sequence, and/or atransmembrane domain and/or a C-terminal anchor domain. In a preferredaspect the immunogenic fragment of BASB119 according to the inventioncomprises substantially all of the extracellular domain of a polypeptidewhich has at least 85% identity, preferably at least 90% identity, morepreferably at least 95% identity, most preferably at least 97-99%identity, to that of SEQ ID NO:2 or 4 over the entire length of SEQ IDNO:2

A fragment is a polypeptide having an amino acid sequence that isentirely the same as part but not all of any amino acid sequence of anypolypeptide of the invention. As with BASB119 polypeptides, fragmentsmay be “free-standing,” or comprised within a larger polypeptide ofwhich they form a part or region, most preferably as a single continuousregion in a single larger polypeptide.

Preferred fragments include, for example, truncation polypeptides havinga portion of an amino acid sequence of SEQ ID NO:2 or 4 or of variantsthereof, such as a continuous series of residues that includes an amino-and/or carboxyl-terminal amino acid sequence. Degradation forms of thepolypeptides of the invention produced by or in a host cell, are alsopreferred. Further preferred are fragments characterized by structuralor functional attributes such as fragments that comprise alpha-helix andalpha-helix forming regions, beta-sheet and beta-sheet-forming regions,turn and turn-forming regions, coil and coil-forming regions,hydrophilic regions, hydrophobic regions, alpha amphipathic regions,beta amphipathic regions, flexible regions, surface-forming regions,substrate binding region, and high antigenic index regions.

Further preferred fragments include an isolated polypeptide comprisingan amino acid sequence having at least 15, 20, 30, 40, 50 or 100contiguous amino acids from the amino acid sequence of SEQ ID NO:2 or 4,or an isolated polypeptide comprising an amino acid sequence having atleast 15, 20, 30, 40, 50 or 100 contiguous amino acids truncated ordeleted from the amino acid sequence of SEQ ID NO:2 or 4.

Fragments of the polypeptides of the invention may be employed forproducing the corresponding full-length polypeptide by peptidesynthesis; therefore, these fragments may be employed as intermediatesfor producing the full-length polypeptides of the invention.

Particularly preferred are variants in which several, 5-10, 1-5, 1-3,1-2 or 1 amino acids are substituted, deleted, or added in anycombination.

The polypeptides, or immunogenic fragments, of the invention may be inthe form of the “mature” protein or may be a part of a larger proteinsuch as a precursor or a fusion protein. It is often advantageous toinclude an additional amino acid sequence which contains secretory orleader sequences, pro-sequences, sequences which aid in purificationsuch as multiple histidine residues, or an additional sequence forstability during recombinant production. Furthermore, addition ofexogenous polypeptide or lipid tail or polynucleotide sequences toincrease the immunogenic potential of the final molecule is alsoconsidered.

In one aspect, the invention relates to genetically engineered solublefusion proteins comprising a polypeptide of the present invention, or afragment thereof, and various portions of the constant regions of heavyor light chains of immunoglobulins of various subclasses (IgG, IgM, IgA,IgE). Preferred as an immunoglobulin is the constant part of the heavychain of human IgG, particularly IgG1, where fusion takes place at thehinge region. In a particular embodiment, the Fc part can be removedsimply by incorporation of a cleavage sequence which can be cleaved withblood clotting factor Xa.

Furthermore, this invention relates to processes for the preparation ofthese fusion proteins by genetic engineering, and to the use thereof fordrug screening, diagnosis and therapy. A further aspect of the inventionalso relates to polynucleotides encoding such fusion proteins. Examplesof fusion protein technology can be found in International PatentApplication Nos. WO94/29458 and WO94/22914.

The proteins may be chemically conjugated, or expressed as recombinantfusion proteins allowing increased levels to be produced in anexpression system as compared to non-fused protein. The fusion partnermay assist in providing T helper epitopes (immunological fusionpartner), preferably T helper epitopes recognised by humans, or assistin expressing the protein (expression enhancer) at higher yields thanthe native recombinant protein. Preferably the fusion partner will beboth an immunological fusion partner and expression enhancing partner.

Fusion partners include protein D from Haemophilus influenzae and thenon-structural protein from influenzae virus, NS1 (hemagglutinin).Another fusion partner is the protein known as LytA. Preferably the Cterminal portion of the molecule is used. Lyta is derived fromStreptococcus pneumoniae which synthesize an N-acetyl-L-alanine amidase,amidase LytA, (coded by the lytA gene {Gene, 43 (1986) page 265-272}) anautolysin that specifically degrades certain bonds in the peptidoglycanbackbone. The C-terminal domain of the LytA protein is responsible forthe affinity to the choline or to some choline analogues such as DEAE.This property has been exploited for the development of E. coli C-LytAexpressing plasmids useful for expression of fusion proteins.Purification of hybrid proteins containing the C-LytA fragment at itsamino terminus has been described {Biotechnology: 10, (1992) page795-798}. It is possible to use the repeat portion of the LytA moleculefound in the C terminal end starting at residue 178, for exampleresidues 188-305.

The present invention also includes variants of the aforementionedpolypeptides, that is polypeptides that vary from the referents byconservative amino acid substitutions, whereby a residue is substitutedby another with like characteristics. Typical such substitutions areamong Ala, Val, Leu and Ile; among Ser and Thr; among the acidicresidues Asp and Glu; among Asn and Gln; and among the basic residuesLys and Arg; or aromatic residues Phe and Tyr.

Polypeptides of the present invention can be prepared in any suitablemanner. Such polypeptides include isolated naturally occurringpolypeptides, recombinantly produced polypeptides, syntheticallyproduced polypeptides, or polypeptides produced by a combination ofthese methods. Means for preparing such polypeptides are well understoodin the art.

It is most preferred that a polypeptide of the invention is derived fromMoraxella catarrhalis, however, it may preferably be obtained from otherorganisms of the same taxonomic genus. A polypeptide of the inventionmay also be obtained, for example, from organisms of the same taxonomicfamily or order.

Polynucleotides

It is an object of the invention to provide polynucleotides that encodeBASB119 polypeptides, particularly polynucleotides that encode thepolypeptide herein designated BASB119.

In a particularly preferred embodiment of the invention thepolynucleotide comprises a region encoding BASB119 polypeptidescomprising a sequence set out in SEQ ID NO:1 or 3 which includes a fulllength gene, or a variant thereof.

The BASB119 polynucleotides provided in SEQ ID NO:1 or 3 are the BASB119polynucleotides from Moraxella catarrhalis strain Mc2931 (ATCC 43617).

As a further aspect of the invention there are provided isolated nucleicacid molecules encoding and/or expressing BASB119 polypeptides andpolynucleotides, particularly Moraxella catarrhalis BASB119 polypeptidesand polynucleotides, including, for example, unprocessed RNAs, ribozymeRNAs, mRNAs, cDNAs, genomic DNAs, B- and Z-DNAs. Further embodiments ofthe invention include biologically, diagnostically, prophylactically,clinically or therapeutically useful polynucleotides and polypeptides,and variants thereof, and compositions comprising the same.

Another aspect of the invention relates to isolated polynucleotides,including at least one full length gene, that encodes a BASB119polypeptide having a deduced amino acid sequence of SEQ ID NO:2 or 4 andpolynucleotides closely related thereto and variants thereof.

In another particularly preferred embodiment of the invention there is aBASB119 polypeptide from Moraxella catarrhalis comprising or consistingof an amino acid sequence of SEQ ID NO:2 or 4 or a variant thereof.

Using the information provided herein, such as a polynucleotide sequenceset out in SEQ ID NO:1 or 3, a polynucleotide of the invention encodingBASB119 polypeptide may be obtained using standard cloning and screeningmethods, such as those for cloning and sequencing chromosomal DNAfragments from bacteria using Moraxella catarrhalis Catlin cells asstarting material, followed by obtaining a full length clone. Forexample, to obtain a polynucleotide sequence of the invention, such as apolynucleotide sequence given in SEQ ID NO:1 or 3, typically a libraryof clones of chromosomal DNA of Moraxella catarrhalis Catlin in E. colior some other suitable host is probed with a radiolabeledoligonucleotide, preferably a 17-mer or longer, derived from a partialsequence. Clones carrying DNA identical to that of the probe can then bedistinguished using stringent hybridization conditions. By sequencingthe individual clones thus identified by hybridization with sequencingprimers designed from the original polypeptide or polynucleotidesequence it is then possible to extend the polynucleotide sequence inboth directions to determine a full length gene sequence. Conveniently,such sequencing is performed, for example, using denatured doublestranded DNA prepared from a plasmid clone. Suitable techniques aredescribed by Maniatis, T., Fritsch, E. F. and Sambrook et al., MOLECULARCLONING, A LABORATORY MANUAL, 2nd Ed.; Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y. (1989). (see in particular Screening ByHybridization 1.90 and Sequencing Denatured Double-Stranded DNATemplates 13.70). Direct genomic DNA sequencing may also be performed toobtain a full length gene sequence. Illustrative of the invention, eachpolynucleotide set out in SEQ ID NO:1 or 3 was discovered in a DNAlibrary derived from Moraxella catarrhalis.

Moreover, each DNA sequence set out in SEQ ID NO:1 or 3 contains an openreading frame encoding a protein having about the number of amino acidresidues set forth in SEQ ID NO:2 or 4 with a deduced molecular weightthat can be calculated using amino acid residue molecular weight valueswell known to those skilled in the art.

The polynucleotide of SEQ ID NO:1, between the start codon at nucleotidenumber 1 and the stop codon which begins at nucleotide number 514 of SEQID NO:1, encodes the polypeptide of SEQ ID NO:2.

The polynucleotide of SEQ ID NO:3, between the start codon at nucleotidenumber 1 and the last codon which begins at nucleotide number 511 of SEQID NO:3, encodes the polypeptide of SEQ ID NO:4.

In a further aspect, the present invention provides for an isolatedpolynucleotide comprising or consisting of:

(a) a polynucleotide sequence which has at least 85% identity,preferably at least 90% identity, more preferably at least 95% identity,even more preferably at least 97-99% or exact identity to SEQ ID NO:1 or3 over the entire length of SEQ ID NO:1 or 3 respectively; or(b) a polynucleotide sequence encoding a polypeptide which has at least85% identity, preferably at least 90% identity, more preferably at least95% identity, even more preferably at least 97-99% or 100% exact, to theamino acid sequence of SEQ ID NO:2 or 4, over the entire length of SEQID NO:2 or 4 respectively.

A polynucleotide encoding a polypeptide of the present invention,including homologs and orthologs from species other than Moraxellacatarrhalis, may be obtained by a process which comprises the steps ofscreening an appropriate library under stringent hybridizationconditions (for example, using a temperature in the range of 45-65° C.and an SDS concentration from 0.1-1%) with a labeled or detectable probeconsisting of or comprising the sequence of SEQ ID NO:1 or 3 or afragment thereof, and isolating a full-length gene and/or genomic clonescontaining said polynucleotide sequence.

The invention provides a polynucleotide sequence identical over itsentire length to a coding sequence (open reading frame) in SEQ ID NO:1or 3. Also provided by the invention is a coding sequence for a maturepolypeptide or a fragment thereof, by itself as well as a codingsequence for a mature polypeptide or a fragment in reading frame withanother coding sequence, such as a sequence encoding a leader orsecretory sequence, a pre-, or pro- or prepro-protein sequence. Thepolynucleotide of the invention may also contain at least one non-codingsequence, including for example, but not limited to at least onenon-coding 5′ and 3′ sequence, such as the transcribed butnon-translated sequences, termination signals (such as rho-dependent andrho-independent termination signals), ribosome binding sites, Kozaksequences, sequences that stabilize in RNA, introns, and polyadenylationsignals. The polynucleotide sequence may also comprise additional codingsequence encoding additional amino acids. For example, a marker sequencethat facilitates purification of the fused polypeptide can be encoded.In certain embodiments of the invention, the marker sequence is ahexa-histidine peptide, as provided in the pQE vector (Qiagen, Inc.) anddescribed in Gentz et al., Proc. Natl. Acad. Sci., USA 86: 821-824(1989), or an HA peptide tag (Wilson et al., Cell 377: 767 (1984), bothof which may be useful in purifying polypeptide sequence fused to them.Polynucleotides of the invention also include, but are not limited to,polynucleotides comprising a structural gene and its naturallyassociated sequences that control gene expression.

The nucleotide sequence encoding BASB119 polypeptide of SEQ ID NO:2 or 4may be identical to the polypeptide encoding sequence contained innucleotides 1 to 513 of SEQ ID NO:1 or the polypeptide encoding sequencecontained in nucleotides 1 to 513 of SEQ ID NO:3 respectively.Alternatively it may be a sequence, which as a result of the redundancy(degeneracy) of the genetic code, also encodes the polypeptide of SEQ IDNO:2 or 4.

The term “polynucleotide encoding a polypeptide” as used hereinencompasses polynucleotides that include a sequence encoding apolypeptide of the invention, particularly a bacterial polypeptide andmore particularly a polypeptide of the Moraxella catarrhalis BASB119having an amino acid sequence set out in SEQ ID NO:2 or 4. The term alsoencompasses polynucleotides that include a single continuous region ordiscontinuous regions encoding the polypeptide (for example,polynucleotides interrupted by integrated phage, an integrated insertionsequence, an integrated vector sequence, an integrated transposonsequence, or due to RNA editing or genomic DNA reorganization) togetherwith additional regions, that also may contain coding and/or non-codingsequences.

The invention further relates to variants of the polynucleotidesdescribed herein that encode variants of a polypeptide having a deducedamino acid sequence of SEQ ID NO:2 or 4. Fragments of polynucleotides ofthe invention may be used, for example, to synthesize full-lengthpolynucleotides of the invention.

Further particularly preferred embodiments are polynucleotides encodingBASB119 variants, that have the amino acid sequence of BASB119polypeptide of SEQ ID NO:2 or 4 in which several, a few, 5 to 10, 1 to5, 1 to 3, 2, 1 or no amino acid residues are substituted, modified,deleted and/or added, in any combination. Especially preferred amongthese are silent substitutions, additions and deletions, that do notalter the properties and activities of BASB119 polypeptide.

Further preferred embodiments of the invention are polynucleotides thatare at least 85% identical over their entire length to a polynucleotideencoding BASB119 polypeptide having an amino acid sequence set out inSEQ ID NO:2 or 4, and polynucleotides that are complementary to suchpolynucleotides. Alternatively, most highly preferred arepolynucleotides that comprise a region that is at least 90% identicalover its entire length to a polynucleotide encoding BASB119 polypeptideand polynucleotides complementary thereto. In this regard,polynucleotides at least 95% identical over their entire length to thesame are particularly preferred. Furthermore, those with at least 97%are highly preferred among those with at least 95%, and among thesethose with at least 98% and at least 99% are particularly highlypreferred, with at least 99% being the more preferred.

Preferred embodiments are polynucleotides encoding polypeptides thatretain substantially the same biological function or activity as themature polypeptide encoded by a DNA of SEQ ID NO:1 or 3.

In accordance with certain preferred embodiments of this invention thereare provided polynucleotides that hybridize, particularly understringent conditions, to BASB119 polynucleotide sequences, such as thosepolynucleotides in SEQ ID NO:1 or 3.

The invention further relates to polynucleotides that hybridize to thepolynucleotide sequences provided herein. In this regard, the inventionespecially relates to polynucleotides that hybridize under stringentconditions to the polynucleotides described herein. As herein used, theterms “stringent conditions” and “stringent hybridization conditions”mean hybridization occurring only if there is at least 95% andpreferably at least 97% identity between the sequences. A specificexample of stringent hybridization conditions is overnight incubation at42° C. in a solution comprising: 50% formamide, 5×SSC (150 mM NaCl, 15mM trisodium citrate), 50 mM sodium phosphate (pH7.6), 5×Denhardt'ssolution, 10% dextran sulfate, and 20 micrograms/ml of denatured,sheared salmon sperm DNA, followed by washing the hybridization supportin 0.1×SSC at about 65° C. Hybridization and wash conditions are wellknown and exemplified in Sambrook, et al., Molecular Cloning: ALaboratory Manual, Second Edition, Cold Spring Harbor, N.Y., (1989),particularly Chapter 11 therein. Solution hybridization may also be usedwith the polynucleotide sequences provided by the invention.

The invention also provides a polynucleotide consisting of or comprisinga polynucleotide sequence obtained by screening an appropriate librarycontaining the complete gene for a polynucleotide sequence set forth inSEQ ID NO: 1 or 3 under stringent hybridization conditions with a probehaving the sequence of said polynucleotide sequence set forth in SEQ IDNO:1 or 3 or a fragment thereof, and isolating said polynucleotidesequence. Fragments useful for obtaining such a polynucleotide include,for example, probes and primers fully described elsewhere herein.

As discussed elsewhere herein regarding polynucleotide assays of theinvention, for instance, the polylucleotides of the invention, may beused as a hybridization probe for RNA, cDNA and genomic DNA to isolatefull-length cDNAs and genomic clones encoding BASB119 and to isolatecDNA and genomic clones of other genes that have a high identity,particularly high sequence identity, to the BASB119 gene. Such probesgenerally will comprise at least 15 nucleotide residues or base pairs.Preferably, such probes will have at least 30 nucleotide residues orbase pairs and may have at least 50 nucleotide residues or base pairs.Particularly preferred probes will have at least 20 nucleotide residuesor base pairs and will have less than 30 nucleotide residues or basepairs.

A coding region of a BASB119 gene may be isolated by screening using aDNA sequence provided in SEQ ID NO:1 or 3 to synthesize anoligonucleotide probe. A labeled oligonucleotide having a sequencecomplementary to that of a gene of the invention is then used to screena library of cDNA, genomic DNA or mRNA to determine which members of thelibrary the probe hybridizes to.

There are several methods available and well known to those skilled inthe art to obtain full-length DNAs, or extend short DNAs, for examplethose based on the method of Rapid Amplification of cDNA ends (RACE)(see, for example, Frohman, et al., PNAS USA 85: 8998-9002, 1988).Recent modifications of the technique, exemplified by the Marathon™technology (Clontech Laboratories Inc.) for example, have significantlysimplified the search for longer cDNAs. In the Marathon™ technology,cDNAs have been prepared from mRNA extracted from a chosen tissue and an‘adaptor’ sequence ligated onto each end. Nucleic acid amplification(PCR) is then carried out to amplify the “missing” 5′ end of the DNAusing a combination of gene specific and adaptor specificoligonucleotide primers. The PCR reaction is then repeated using“nested” primers, that is, primers designed to anneal within theamplified product (typically an adaptor specific primer that annealsfurther 3′ in the adaptor sequence and a gene specific primer thatanneals further 5′ in the selected gene sequence). The products of thisreaction can then be analyzed by DNA sequencing and a full-length DNAconstructed either by joining the product directly to the existing DNAto give a complete sequence, or carrying out a separate full-length PCRusing the new sequence information for the design of the 5′ primer.

The polynucleotides and polypeptides of the invention may be employed,for example, as research reagents and materials for discovery oftreatments of and diagnostics for diseases, particularly human diseases,as further discussed herein relating to polynucleotide assays.

The polynucleotides of the invention that are oligonucleotides derivedfrom a sequence of SEQ ID NOS:1 or 3 may be used in the processes hereinas described, but preferably for PCR, to determine whether or not thepolynucleotides identified herein in whole or in part are transcribed inbacteria in infected tissue. It is recognized that such sequences willalso have utility in diagnosis of the stage of infection and type ofinfection the pathogen has attained.

The invention also provides polynucleotides that encode a polypeptidethat is the mature protein plus additional amino or carboxyl-terminalamino acids, or amino acids interior to the mature polypeptide (when themature form has more than one polypeptide chain, for instance). Suchsequences may play a role in processing of a protein from precursor to amature form, may allow protein transport, may lengthen or shortenprotein half-life or may facilitate manipulation of a protein for assayor production, among other things. As generally is the case in vivo, theadditional amino acids may be processed away from the mature protein bycellular enzymes.

For each and every polynucleotide of the invention there is provided apolynucleotide complementary to it. It is preferred that thesecomplementary polynucleotides are fully complementary to eachpolynucleotide with which they are complementary.

A precursor protein, having a mature form of the polypeptide fused toone or more prosequences may be an inactive form of the polypeptide.When prosequences are removed such inactive precursors generally areactivated. Some or all of the prosequences may be removed beforeactivation. Generally, such precursors are called proproteins.

In addition to the standard A, G, C, T/U representations fornucleotides, the term “N” may also be used in describing certainpolynucleotides of the invention. “N” means that any of the four DNA orRNA nucleotides may appear at such a designated position in the DNA orRNA sequence, except it is preferred that N is not a nucleic acid thatwhen taken in combination with adjacent nucleotide positions, when readin the correct reading frame, would have the effect of generating apremature termination codon in such reading frame.

In sum, a polynucleotide of the invention may encode a mature protein, amature protein plus a leader sequence (which may be referred to as apreprotein), a precursor of a mature protein having one or moreprosequences that are not the leader sequences of a preprotein, or apreproprotein, which is a precursor to a proprotein, having a leadersequence and one or more prosequences, which generally are removedduring processing steps that produce active and mature forms of thepolypeptide.

In accordance with an aspect of the invention, there is provided the useof a polynucleotide of the invention for therapeutic or prophylacticpurposes, in particular genetic immunization.

The use of a polynucleotide of the invention in genetic immunizationwill preferably employ a suitable delivery method such as directinjection of plasmid DNA into muscles (Wolff et al., Hum Mol Genet(1992) 1: 363, Manthorpe et al., Hum. Gene Ther. (1983) 4: 419),delivery of DNA complexed with specific protein carriers (Wu et al., JBiol Chem. (1989) 264: 16985), coprecipitation of DNA with calciumphosphate (Benvenisty & Reshef, PNAS USA, (1986) 83: 9551),encapsulation of DNA in various forms of liposomes (Kaneda et al.,Science (1989) 243: 375), particle bombardment (Tang et al., Nature(1992) 356:152, Eisenbraun et al., DNA Cell Biol (1993) 12: 791) and invivo infection using cloned retroviral vectors (Seeger et al., PNAS USA(1984) 81: 5849).

Vectors, Host Cells, Expression Systems

The invention also relates to vectors that comprise a polynucleotide orpolynucleotides of the invention, host cells that are geneticallyengineered with vectors of the invention and the production ofpolypeptides of the invention by recombinant techniques. Cell-freetranslation systems can also be employed to produce such proteins usingRNAs derived from the DNA constructs of the invention.

Recombinant polypeptides of the present invention may be prepared byprocesses well known in those skilled in the art from geneticallyengineered host cells comprising expression systems. Accordingly, in afurther aspect, the present invention relates to expression systems thatcomprise a polynucleotide or polynucleotides of the present invention,to host cells which are genetically engineered with such expressionsystems, and to the production of polypeptides of the invention byrecombinant techniques.

For recombinant production of the polypeptides of the invention, hostcells can be genetically engineered to incorporate expression systems orportions thereof or polynucleotides of the invention. Introduction of apolynucleotide into the host cell can be effected by methods describedin many standard laboratory manuals, such as Davis, et al., BASICMETHODS IN MOLECULAR BIOLOGY, (1986) and Sambrook, et al., MOLECULARCLONING: A LABORATORY MANUAL, 2nd Ed., Cold Spring Harbor LaboratoryPress, Cold Spring Harbor, N.Y. (1989), such as, calcium phosphatetransfection, DEAE-dextran mediated transfection, transvection,microinjection, cationic lipid-mediated transfection, electroporation,transduction, scrape loading, ballistic introduction and infection.

Representative examples of appropriate hosts include bacterial cells,such as cells of streptococci, staphylococci, enterococci, E. coli,streptomyces, cyanobacteria, Bacillus subtilis, Neisseria meningitidisand Moraxella catarrhalis; fungal cells, such as cells of a yeast,Kluveromyces, Saccharomyces, a basidiomycete, Candida albicans andAspergillus; insect cells such as cells of Drosophila S2 and SpodopteraSf9; animal cells such as CHO, COS, HeLa, C127, 3T3, BHK, 293, CV-1 andBowes melanoma cells; and plant cells, such as cells of a gymnosperm orangiosperm.

A great variety of expression systems can be used to produce thepolypeptides of the invention. Such vectors include, among others,chromosomal-, episomal- and virus-derived vectors, for example, vectorsderived from bacterial plasmids, from bacteriophage, from transposons,from yeast episomes, from insertion elements, from yeast chromosomalelements, from viruses such as baculoviruses, papova viruses, such asSV40, vaccinia viruses, adenoviruses, fowl pox viruses, pseudorabiesviruses, picornaviruses, retroviruses, and alphaviruses and vectorsderived from combinations thereof, such as those derived from plasmidand bacteriophage genetic elements, such as cosmids and phagemids. Theexpression system constructs may contain control regions that regulateas well as engender expression. Generally, any system or vector suitableto maintain, propagate or express polynucleotides and/or to express apolypeptide in a host may be used for expression in this regard. Theappropriate DNA sequence may be inserted into the expression system byany of a variety of well-known and routine techniques, such as, forexample, those set forth in Sambrook et al., MOLECULAR CLONING, ALABORATORY MANUAL, (supra).

In recombinant expression systems in eukaryotes, for secretion of atranslated protein into the lumen of the endoplasmic reticulum, into theperiplasmic space or into the extracellular environment, appropriatesecretion signals may be incorporated into the expressed polypeptide.These signals may be endogenous to the polypeptide or they may beheterologous signals.

Polypeptides of the present invention can be recovered and purified fromrecombinant cell cultures by well-known methods including ammoniumsulfate or ethanol precipitation, acid extraction, anion or cationexchange chromatography, phosphocellulose chromatography, hydrophobicinteraction chromatography, affinity chromatography, hydroxylapatitechromatography and lectin chromatography. Most preferably, ion metalaffinity chromatography (IMAC) is employed for purification. Well knowntechniques for refolding proteins may be employed to regenerate activeconformation when the polypeptide is denatured during intracellularsynthesis, isolation and or purification.

The expression system may also be a recombinant live microorganism, suchas a virus or bacterium. The gene of interest can be inserted into thegenome of a live recombinant virus or bacterium. Inoculation and in vivoinfection with this live vector will lead to in vivo expression of theantigen and induction of immune responses. Viruses and bacteria used forthis purpose are for instance: poxviruses (e.g; vaccinia, fowlpox,canarypox), alphaviruses (Sindbis virus, Semliki Forest Virus,Venezuelian Equine Encephalitis Virus), adenoviruses, adeno-associatedvirus, picornaviruses (poliovirus, rhinovirus), herpesviruses (varicellazoster virus, etc), Listeria, Salmonella, Shigella, BCG. These virusesand bacteria can be virulent, or attenuated in various ways in order toobtain live vaccines. Such live vaccines also form part of theinvention.

Diagnostic, Prognostic, Serotyping and Mutation Assays

This invention is also related to the use of BASB119 polynucleotides andpolypeptides of the invention for use as diagnostic reagents. Detectionof BASB119 polynucleotides and/or polypeptides in a eukaryote,particularly a mammal, and especially a human, will provide a diagnosticmethod for diagnosis of disease, staging of disease or response of aninfectious organism to drugs. Eukaryotes, particularly mammals, andespecially humans, particularly those infected or suspected to beinfected with an organism comprising the BASB119 gene or protein, may bedetected at the nucleic acid or amino acid level by a variety of wellknown techniques as well as by methods provided herein.

Polypeptides and polynucleotides for prognosis, diagnosis or otheranalysis may be obtained from a putatively infected and/or infectedindividual's bodily materials. Polynucleotides from any of thesesources, particularly DNA or RNA, may be used directly for detection ormay be amplified enzymatically by using PCR or any other amplificationtechnique prior to analysis. RNA, particularly mRNA, cDNA and genomicDNA may also be used in the same ways. Using amplification,characterization of the species and strain of infectious or residentorganism present in an individual, may be made by an analysis of thegenotype of a selected polynucleotide of the organism. Deletions andinsertions can be detected by a change in size of the amplified productin comparison to a genotype of a reference sequence selected from arelated organism, preferably a different species of the same genus or adifferent strain of the same species. Point mutations can be identifiedby hybridizing amplified DNA to labeled BASB119 polynucleotidesequences. Perfectly or significantly matched sequences can bedistinguished from imperfectly or more significantly mismatched duplexesby DNase or RNase digestion, for DNA or RNA respectively, or bydetecting differences in melting temperatures or renaturation kinetics.Polynucleotide sequence differences may also be detected by alterationsin the electrophoretic mobility of polynucleotide fragments in gels ascompared to a reference sequence. This may be carried out with orwithout denaturing agents. Polynucleotide differences may also bedetected by direct DNA or RNA sequencing. See, for example, Myers etal., Science, 230: 1242 (1985). Sequence changes at specific locationsalso may be revealed by nuclease protection assays, such as RNase, V1and S1 protection assay or a chemical cleavage method. See, for example,Cotton et al., Proc. Natl. Acad. Sci., USA, 85: 4397-4401 (1985).

In another embodiment, an array of oligonucleotides probes comprisingBASB119 nucleotide sequence or fragments thereof can be constructed toconduct efficient screening of, for example, genetic mutations,serotype, taxonomic classification or identification. Array technologymethods are well known and have general applicability and can be used toaddress a variety of questions in molecular genetics including geneexpression, genetic linkage, and genetic variability (see, for example,Chee et al., Science, 274: 610 (1996)).

Thus in another aspect, the present invention relates to a diagnostickit which comprises:

(a) a polynucleotide of the present invention, preferably the nucleotidesequence of SEQ ID NO:1 or 3, or a fragment thereof;(b) a nucleotide sequence complementary to that of (a);(c) a polypeptide of the present invention, preferably the polypeptideof SEQ ID NO:2 or 4 or a fragment thereof, or(d) an antibody to a polypeptide of the present invention, preferably tothe polypeptide of SEQ ID NO:2 or 4.

It will be appreciated that in any such kit, (a), (b), (c) or (d) maycomprise a substantial component. Such a kit will be of use indiagnosing a disease or susceptibility to a Disease, among others.

This invention also relates to the use of polynucleotides of the presentinvention as diagnostic reagents. Detection of a mutated form of apolynucleotide of the invention, preferably SEQ ID NO:1 or 3, which isassociated with a disease or pathogenicity will provide a diagnostictool that can add to, or define, a diagnosis of a disease, a prognosisof a course of disease, a determination of a stage of disease, or asusceptibility to a disease, which results from under-expression,over-expression or altered expression of the polynucleotide. Organisms,particularly infectious organisms, carrying mutations in suchpolynucleotide may be detected at the polynucleotide level by a varietyof techniques, such as those described elsewhere herein.

Cells from an organism carrying mutations or polymorphisms (allelicvariations) in a polynucleotide and/or polypeptide of the invention mayalso be detected at the polynucleotide or polypeptide level by a varietyof techniques, to allow for serotyping, for example. For example, RT-PCRcan be used to detect mutations in the RNA. It is particularly preferredto use RT-PCR in conjunction with automated detection systems, such as,for example, GeneScan. RNA, cDNA or genomic DNA may also be used for thesame purpose, PCR. As an example, PCR primers complementary to apolynucleotide encoding BASB119 polypeptide can be used to identify andanalyze mutations.

The invention further provides primers with 1, 2, 3 or 4 nucleotidesremoved from the 5′ and/or the 3′ end. These primers may be used for,among other things, amplifying BASB119 DNA and/or RNA isolated from asample derived from an individual, such as a bodily material. Theprimers may be used to amplify a polynucleotide isolated from aninfected individual, such that the polynucleotide may then be subject tovarious techniques for elucidation of the polynucleotide sequence. Inthis way, mutations in the polynucleotide sequence may be detected andused to diagnose and/or prognose the infection or its stage or course,or to serotype and/or classify the infectious agent.

The invention further provides a process for diagnosing, disease,preferably bacterial infections, more preferably infections caused byMoraxella catarrhalis, comprising determining from a sample derived froman individual, such as a bodily material, an increased level ofexpression of polynucleotide having a sequence of SEQ ID NO:1 or 3.Increased or decreased expression of a BASB119 polynucleotide can bemeasured using any on of the methods well known in the art for thequantitation of polynucleotides, such as, for example, amplification,PCR, RT-PCR, RNase protection, Northern blotting, spectrometry and otherhybridization methods.

In addition, a diagnostic assay in accordance with the invention fordetecting over-expression of BASB119 polypeptide compared to normalcontrol tissue samples may be used to detect the presence of aninfection, for example. Assay techniques that can be used to determinelevels of a BASB119 polypeptide, in a sample derived from a host, suchas a bodily material, are well-known to those of skill in the art. Suchassay methods include radioimmunoassays, competitive-binding assays,Western Blot analysis, antibody sandwich assays, antibody detection andELISA assays.

The polynucleotides of the invention may be used as components ofpolynucleotide arrays, preferably high density arrays or grids. Thesehigh density arrays are particularly useful for diagnostic andprognostic purposes. For example, a set of spots each comprising adifferent gene, and further comprising a polynucleotide orpolynucleotides of the invention, may be used for probing, such as usinghybridization or nucleic acid amplification, using a probes obtained orderived from a bodily sample, to determine the presence of a particularpolynucleotide sequence or related sequence in an individual. Such apresence may indicate the presence of a pathogen, particularly Moraxellacatarrhalis, and may be useful in diagnosing and/or prognosing diseaseor a course of disease. A grid comprising a number of variants of thepolynucleotide sequence of SEQ ID NO:1 or 3 are preferred. Alsopreferred is a comprising a number of variants of a polynucleotidesequence encoding the polypeptide sequence of SEQ ID NO:2 or 4.

Antibodies

The polypeptides and polynucleotides of the invention or variantsthereof, or cells expressing the same can be used as immunogens toproduce antibodies immunospecific for such polypeptides orpolynucleotides respectively. The term “immunospecific” means that theantibodies have substantially greater affinity for the polypeptides ofthe invention than their affinity for other related polypeptides in theprior art.

In certain preferred embodiments of the invention there are providedantibodies against BASB119 polypeptides or polynucleotides.

Antibodies generated against the polypeptides or polynucleotides of theinvention can be obtained by administering the polypeptides and/orpolynucleotides of the invention, or epitope-bearing fragments of eitheror both, analogues of either or both, or cells expressing either orboth, to an animal, preferably a nonhuman, using routine protocols. Forpreparation of monoclonal antibodies, any technique known in the artthat provides antibodies produced by continuous cell line cultures canbe used. Examples include various techniques, such as those in Kohler,G. and Milstein, C., Nature 256: 495-497 (1975); Kozbor et al.,Immunology Today 4: 72 (1983); Cole et al., pg. 77-96 in MONOCLONALANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc. (1985).

Techniques for the production of single chain antibodies (U.S. Pat. No.4,946,778) can be adapted to produce single chain antibodies topolypeptides or polynucleotides of this invention. Also, transgenicmice, or other organisms or animals, such as other mammals, may be usedto express humanized antibodies immunospecific to the polypeptides orpolynucleotides of the invention.

Alternatively, phage display technology may be utilized to selectantibody genes with binding activities towards a polypeptide of theinvention either from repertoires of PCR amplified v-genes oflymphocytes from humans screened for possessing anti-BASB119 or fromnaive libraries (McCafferty, et al., (1990), Nature 348, 552-554; Marks,et al., (1992) Biotechnology 10, 779-783). The affinity of theseantibodies can also be improved by, for example, chain shuffling(Clackson et al., (1991) Nature 352: 628).

The above-described antibodies may be employed to isolate or to identifyclones expressing the polypeptides or polynucleotides of the inventionto purify the polypeptides or polynucleotides by, for example, affinitychromatography.

Thus, among others, antibodies against BASB119-polypeptide orBASB119-polynucleotide may be employed to treat infections, particularlybacterial infections.

Polypeptide variants include antigenically, epitopically orimmunologically equivalent variants form a particular aspect of thisinvention.

Preferably, the antibody or variant thereof is modified to make it lessimmunogenic in the individual. For example, if the individual is humanthe antibody may most preferably be “humanized,” where thecomplimentarily determining region or regions of the hybridoma-derivedantibody has been transplanted into a human monoclonal antibody, forexample as described in Jones et al. (1986), Nature 321, 522-525 orTempest et al., (1991) Biotechnology 9, 266-273.

Antagonists and Agonists—Assays and Molecules

Polypeptides and polynucleotides of the invention may also be used toassess the binding of small molecule substrates and ligands in, forexample, cells, cell-free preparations, chemical libraries, and naturalproduct mixtures. These substrates and ligands may be natural substratesand ligands or may be structural or functional mimetics. See, e.g.,Coligan et al., Current Protocols in Immunology 1(2). Chapter 5 (1991).

The screening methods may simply measure the binding of a candidatecompound to the polypeptide or polynucleotide, or to cells or membranesbearing the polypeptide or polynucleotide, or a fusion protein of thepolypeptide by means of a label directly or indirectly associated withthe candidate compound. Alternatively, the screening method may involvecompetition with a labeled competitor. Further, these screening methodsmay test whether the candidate compound results in a signal generated byactivation or inhibition of the polypeptide or polynucleotide, usingdetection systems appropriate to the cells comprising the polypeptide orpolynucleotide. Inhibitors of activation are generally assayed in thepresence of a known agonist and the effect on activation by the agonistby the presence of the candidate compound is observed. Constitutivelyactive polypeptide and/or constitutively expressed polypeptides andpolynucleotides may be employed in screening methods for inverseagonists or inhibitors, in the absence of an agonist or inhibitor, bytesting whether the candidate compound results in inhibition ofactivation of the polypeptide or polynucleotide, as the case may be.Further, the screening methods may simply comprise the steps of mixing acandidate compound with a solution containing a polypeptide orpolynucleotide of the present invention, to form a mixture, measuringBASB119 polypeptide and/or polynucleotide activity in the mixture, andcomparing the BASB119 polypeptide and/or polynucleotide activity of themixture to a standard. Fusion proteins, such as those made from Fcportion and BASB119 polypeptide, as hereinbefore described, can also beused for high-throughput screening assays to identify antagonists of thepolypeptide of the present invention, as well as of phylogeneticallyand/or functionally related polypeptides (see D. Bennett et al., J MolRecognition, 8:52-58 (1995); and K. Johanson et al., J Biol Chem,270(16):9459-9471 (1995)).

The polynucleotides, polypeptides and antibodies that bind to and/orinteract with a polypeptide of the present invention may also be used toconfigure screening methods for detecting the effect of added compoundson the production of mRNA and/or polypeptide in cells. For example, anELISA assay may be constructed for measuring secreted or cell associatedlevels of polypeptide using monoclonal and polyclonal antibodies bystandard methods known in the art. This can be used to discover agentswhich may inhibit or enhance the production of polypeptide (also calledantagonist or agonist, respectively) from suitably manipulated cells ortissues.

The invention also provides a method of screening compounds to identifythose which enhance (agonist) or block (antagonist) the action ofBASB119 polypeptides or polynucleotides, particularly those compoundsthat are bacteriostatic and/or bactericidal. The method of screening mayinvolve high-throughput techniques. For example, to screen for agonistsor antagonists, a synthetic reaction mix, a cellular compartment, suchas a membrane, cell envelope or cell wall, or a preparation of anythereof, comprising BASB119 polypeptide and a labeled substrate orligand of such polypeptide is incubated in the absence or the presenceof a candidate molecule that may be a BASB119 agonist or antagonist. Theability of the candidate molecule to agonize or antagonize the BASB119polypeptide is reflected in decreased binding of the labeled ligand ordecreased production of product from such substrate. Molecules that bindgratuitously, i.e., without inducing the effects of BASB119 polypeptideare most likely to be good antagonists. Molecules that bind well and, asthe case may be, increase the rate of product production from substrate,increase signal transduction, or increase chemical channel activity areagonists. Detection of the rate or level of, as the case may be,production of product from substrate, signal transduction, or chemicalchannel activity may be enhanced by using a reporter system. Reportersystems that may be useful in this regard include but are not limited tocalorimetric, labeled substrate converted into product, a reporter genethat is responsive to changes in BASB119 polynucleotide or polypeptideactivity, and binding assays known in the art.

Another example of an assay for BASB119 agonists is a competitive assaythat combines BASB119 and a potential agonist with BASB119-bindingmolecules, recombinant BASB119 binding molecules, natural substrates orligands, or substrate or ligand mimetics, under appropriate conditionsfor a competitive inhibition assay. BASB119 can be labeled, such as byradioactivity or a calorimetric compound, such that the number ofBASB119 molecules bound to a binding molecule or converted to productcan be determined accurately to assess the effectiveness of thepotential antagonist.

Potential antagonists include, among others, small organic molecules,peptides, polypeptides and antibodies that bind to a polynucleotideand/or polypeptide of the invention and thereby inhibit or extinguishits activity or expression. Potential antagonists also may be smallorganic molecules, a peptide, a polypeptide such as a closely relatedprotein or antibody that binds the same sites on a binding molecule,such as a binding molecule, without inducing BASB119-induced activities,thereby preventing the action or expression of BASB119 polypeptidesand/or polynucleotides by excluding BASB119 polypeptides and/orpolynucleotides from binding.

Potential antagonists include a small molecule that binds to andoccupies the binding site of the polypeptide thereby preventing bindingto cellular binding molecules, such that normal biological activity isprevented. Examples of small molecules include but are not limited tosmall organic molecules, peptides or peptide-like molecules. Otherpotential antagonists include antisense molecules (see Okano, J.Neurochem. 56: 560 (1991); OLIGODEOXYNUCLEOTIDES AS ANTISENSE INHIBITORSOF GENE EXPRESSION, CRC Press, Boca Raton, Fla. (1988), for adescription of these molecules). Preferred potential antagonists includecompounds related to and variants of BASB119.

In a further aspect, the present invention relates to geneticallyengineered soluble fusion proteins comprising a polypeptide of thepresent invention, or a fragment thereof, and various portions of theconstant regions of heavy or light chains of immunoglobulins of varioussubclasses (IgG, IgM, IgA, IgE). Preferred as an immunoglobulin is theconstant part of the heavy chain of human IgG, particularly IgG1, wherefusion takes place at the hinge region. In a particular embodiment, theFc part can be removed simply by incorporation of a cleavage sequencewhich can be cleaved with blood clotting factor Xa. Furthermore, thisinvention relates to processes for the preparation of these fusionproteins by genetic engineering, and to the use thereof for drugscreening, diagnosis and therapy. A further aspect of the invention alsorelates to polynucleotides encoding such fusion proteins. Examples offusion protein technology can be found in International PatentApplication Nos. WO94/29458 and WO94/22914.

Each of the polynucleotide sequences provided herein may be used in thediscovery and development of antibacterial compounds. The encodedprotein, upon expression, can be used as a target for the screening ofantibacterial drugs. Additionally, the polynucleotide sequences encodingthe amino terminal regions of the encoded protein or Shine-Delgarno orother translation facilitating sequences of the respective mRNA can beused to construct antisense sequences to control the expression of thecoding sequence of interest.

The invention also provides the use of the polypeptide, polynucleotide,agonist or antagonist of the invention to interfere with the initialphysical interaction between a pathogen or pathogens and a eukaryotic,preferably mammalian, host responsible for sequelae of infection. Inparticular, the molecules of the invention may be used: in theprevention of adhesion of bacteria, in particular gram positive and/orgram negative bacteria, to eukaryotic, preferably mammalian,extracellular matrix proteins on in-dwelling devices or to extracellularmatrix proteins in wounds; to block bacterial adhesion betweeneukaryotic, preferably mammalian, extracellular matrix proteins andbacterial BASB119 proteins that mediate tissue damage and/or; to blockthe normal progression of pathogenesis in infections initiated otherthan by the implantation of in-dwelling devices or by other surgicaltechniques.

In accordance with yet another aspect of the invention, there areprovided BASB119 agonists and antagonists, preferably bacteriostatic orbactericidal agonists and antagonists.

The antagonists and agonists of the invention may be employed, forinstance, to prevent, inhibit and/or treat diseases.

In a further aspect, the present invention relates to mimotopes of thepolypeptide of the invention. A mimotope is a peptide sequence,sufficiently similar to the native peptide (sequentially orstructurally), which is capable of being recognised by antibodies whichrecognise the native peptide; or is capable of raising antibodies whichrecognise the native peptide when coupled to a suitable carrier.

Peptide mimotopes may be designed for a particular purpose by addition,deletion or substitution of elected amino acids. Thus, the peptides maybe modified for the purposes of ease of conjugation to a proteincarrier. For example, it may be desirable for some chemical conjugationmethods to include a terminal cysteine. In addition it may be desirablefor peptides conjugated to a protein carrier to include a hydrophobicterminus distal from the conjugated terminus of the peptide, such thatthe free unconjugated end of the peptide remains associated with thesurface of the carrier protein. Thereby presenting the peptide in aconformation which most closely resembles that of the peptide as foundin the context of the whole native molecule. For example, the peptidesmay be altered to have an N-terminal cysteine and a C-terminalhydrophobic amidated tail. Alternatively, the addition or substitutionof a D-stereoisomer form of one or more of the amino acids may beperformed to create a beneficial derivative, for example to enhancestability of the peptide.

Alternatively, peptide mimotopes may be identified using antibodieswhich are capable themselves of binding to the polypeptides of thepresent invention using techniques such as phage display technology (EP0 552 267 B1). This technique, generates a large number of peptidesequences which mimic the structure of the native peptides and are,therefore, capable of binding to anti-native peptide antibodies, but maynot necessarily themselves share significant sequence homology to thenative polypeptide.

Vaccines

Another aspect of the invention relates to a method for inducing animmunological response in an individual, particularly a mammal,preferably humans, which comprises inoculating the individual withBASB119 polynucleotide and/or polypeptide, or a fragment or variantthereof, adequate to produce antibody and/or T cell immune response toprotect said individual from infection, particularly bacterial infectionand most particularly Moraxella catarrhalis infection. Also provided aremethods whereby such immunological response slows bacterial replication.Yet another aspect of the invention relates to a method of inducingimmunological response in an individual which comprises delivering tosuch individual a nucleic acid vector, sequence or ribozyme to directexpression of BASB119 polynucleotide and/or polypeptide, or a fragmentor a variant thereof, for expressing BASB119 polynucleotide and/orpolypeptide, or a fragment or a variant thereof in vivo in order toinduce an immunological response, such as, to produce antibody and/or Tcell immune response, including, for example, cytokine-producing T cellsor cytotoxic T cells, to protect said individual, preferably a human,from disease, whether that disease is already established within theindividual or not. One example of administering the gene is byaccelerating it into the desired cells as a coating on particles orotherwise. Such nucleic acid vector may comprise DNA, RNA, a ribozyme, amodified nucleic acid, a DNA/RNA hybrid, a DNA-protein complex or anRNA-protein complex.

A further aspect of the invention relates to an immunologicalcomposition that when introduced into an individual, preferably a human,capable of having induced within it an immunological response, inducesan immunological response in such individual to a BASB119 polynucleotideand/or polypeptide encoded therefrom, wherein the composition comprisesa recombinant BASB119 polynucleotide and/or polypeptide encodedtherefrom and/or comprises DNA and/or RNA which encodes and expresses anantigen of said BASB119 polynucleotide, polypeptide encoded therefrom,or other polypeptide of the invention. The immunological response may beused therapeutically or prophylactically and may take the form ofantibody immunity and/or cellular immunity, such as cellular immunityarising from CTL or CD4+ T cells.

A BASB119 polypeptide or a fragment thereof may be fused with co-proteinor chemical moiety which may or may not by itself produce antibodies,but which is capable of stabilizing the first protein and producing afused or modified protein which will have antigenic and/or immunogenicproperties, and preferably protective properties. Thus fused recombinantprotein, preferably further comprises an antigenic co-protein, such aslipoprotein D from Haemophilus influenzae, Glutathione-S-transferase(GST) or beta-galactosidase, or any other relatively large co-proteinwhich solubilizes the protein and facilitates production andpurification thereof. Moreover, the co-protein may act as an adjuvant inthe sense of providing a generalized stimulation of the immune system ofthe organism receiving the protein. The co-protein may be attached toeither the amino- or carboxy-terminus of the first protein.

In a vaccine composition according to the invention, a BASB119polypeptide and/or polynucleotide, or a fragment, or a mimotope, or avariant thereof may be present in a vector, such as the live recombinantvectors described above for example live bacterial vectors.

Also suitable are non-live vectors for the BASB119 polypeptide, forexample bacterial outer-membrane vesicles or “blebs”. OM blebs arederived from the outer membrane of the two-layer membrane ofGram-negative bacteria and have been documented in many Gram-negativebacteria (Zhou, L et al. 1998. FEMS Microbiol. Lett. 163:223-228)including C. trachomatis and C. psittaci. A non-exhaustive list ofbacterial pathogens reported to produce blebs also includes: Bordetellapertussis, Borrelia burgdorferi, Brucella melitensis, Brucella ovis,Esherichia coli, Haemophilus influenza, Legionella pneumophila,Moraxella catarrhalis, Neisseria gonorrhoeae, Neisseria meningitidis,Pseudomonas aeruginosa and Yersinia enterocolitica.

Blebs have the advantage of providing outer-membrane proteins in theirnative conformation and are thus particularly useful for vaccines. Blebscan also be improved for vaccine use by engineering the bacterium so asto modify the expression of one or more molecules at the outer membrane.Thus for example the expression of a desired immunogenic protein at theouter membrane, such as the BASB119 polypeptide, can be introduced orupregulated (e.g. by altering the promoter). Instead or in addition, theexpression of outer-membrane molecules which are either not relevant(e.g. unprotective antigens or immunodominant but variable proteins) ordetrimental (e.g. toxic molecules such as LPS, or potential inducers ofan autoimmune response) can be downregulated. These approaches arediscussed in more detail below.

The non-coding flanking regions of the BASB119 gene contain regulatoryelements important in the expression of the gene. This regulation takesplace both at the transcriptional and translational level. The sequenceof these regions, either upstream or downstream of the open readingframe of the gene, can be obtained by DNA sequencing. This sequenceinformation allows the determination of potential regulatory motifs suchas the different promoter elements, terminator sequences, induciblesequence elements, repressors, elements responsible for phase variation,the shine-dalgarno sequence, regions with potential secondary structureinvolved in regulation, as well as other types of regulatory motifs orsequences. This sequence is a further aspect of the invention.

This sequence information allows the modulation of the naturalexpression of the BASB119 gene. The upregulation of the gene expressionmay be accomplished by altering the promoter, the shine-dalgarnosequence, potential repressor or operator elements, or any otherelements involved. Likewise, downregulation of expression can beachieved by similar types of modification. Alternatively, by changingphase variation sequences, the expression of the gene can be put underphase variation control, or it may be uncoupled from this regulation. Inanother approach, the expression of the gene can be put under thecontrol of one or more inducible elements allowing regulated expression.Examples of such regulation include, but are not limited to, inductionby temperature shift, addition of inductor substrates like selectedcarbohydrates or their derivatives, trace elements, vitamins,co-factors, metal ions, etc.

Such modifications as described above can be introduced by severaldifferent means. The modification of sequences involved in geneexpression can be carried out in vivo by random mutagenesis followed byselection for the desired phenotype. Another approach consists inisolating the region of interest and modifying it by random mutagenesis,or site-directed replacement, insertion or deletion mutagenesis. Themodified region can then be reintroduced into the bacterial genome byhomologous recombination, and the effect on gene expression can beassessed. In another approach, the sequence knowledge of the region ofinterest can be used to replace or delete all or part of the naturalregulatory sequences. In this case, the regulatory region targeted isisolated and modified so as to contain the regulatory elements fromanother gene, a combination of regulatory elements from different genes,a synthetic regulatory region, or any other regulatory region, or todelete selected parts of the wild-type regulatory sequences. Thesemodified sequences can then be reintroduced into the bacterium viahomologous recombination into the genome. A non-exhaustive list ofpreferred promoters that could be used for up-regulation of geneexpression includes the promoters porA, porB, lbpB, tbpB, p110, lst,hpuAB from N. meningitidis or N. gonorroheae, ompCD, copB, lbpB, ompE,UspA1; UspA2; TbpB from M. Catarrhalis, p1, p2, p4, p5, p6, lpD, tbpB,D15, Hia, Hmw1, Hmw2 from H. influenzae.

In one example, the expression of the gene can be modulated byexchanging its promoter with a stronger promoter (through isolating theupstream sequence of the gene, in vitro modification of this sequence,and reintroduction into the genome by homologous recombination).Upregulated expression can be obtained in both the bacterium as well asin the outer membrane vesicles shed (or made) from the bacterium.

In other examples, the described approaches can be used to generaterecombinant bacterial strains with improved characteristics for vaccineapplications. These can be, but are not limited to, attenuated strains,strains with increased expression of selected antigens, strains withknock-outs (or decreased expression) of genes interfering with theimmune response, strains with modulated expression of immunodominantproteins, strains with modulated shedding of outer-membrane vesicles.

Thus, also provided by the invention is a modified upstream region ofthe BASB119 gene, which modified upstream region contains a heterologousregulatory element which alters the expression level of the BASB119protein located at the outer membrane. The upstream region according tothis aspect of the invention includes the sequence upstream of theBASB119 gene. The upstream region starts immediately upstream of theBASB119 gene and continues usually to a position no more than about 1000bp upstream of the gene from the ATG start codon. In the case of a genelocated in a polycistronic sequence (operon) the upstream region canstart immediately preceding the gene of interest, or preceding the firstgene in the operon. Preferably, a modified upstream region according tothis aspect of the invention contains a heterologous promotor at aposition between 500 and 700 bp upstream of the ATG.

Thus, the invention provides a BASB119 polypeptide, in a modifiedbacterial bleb. The invention further provides modified host cellscapable of producing the non-live membrane-based bleb vectors. Theinvention further provides nucleic acid vectors comprising the BASB119gene having a modified upstream region containing a heterologousregulatory element.

Further provided by the invention are processes to prepare the hostcells and bacterial blebs according to the invention.

Also provided by this invention are compositions, particularly vaccinecompositions, and methods comprising the polypeptides and/orpolynucleotides of the invention and immunostimulatory DNA sequences,such as those described in Sato, Y. et al. Science 273: 352 (1996).

Also, provided by this invention are methods using the describedpolynucleotide or particular fragments thereof, which have been shown toencode non-variable regions of bacterial cell surface proteins, inpolynucleotide constructs used in such genetic immunization experimentsin animal models of infection with Moraxella catarrhalis. Suchexperiments will be particularly useful for identifying protein epitopesable to provoke a prophylactic or therapeutic immune response. It isbelieved that this approach will allow for the subsequent preparation ofmonoclonal antibodies of particular value, derived from the requisiteorgan of the animal successfully resisting or clearing infection, forthe development of prophylactic agents or therapeutic treatments ofbacterial infection, particularly Moraxella catarrhalis infection, inmammals, particularly humans.

The invention also includes a vaccine formulation which comprises animmunogenic recombinant polypeptide and/or polynucleotide of theinvention together with a suitable carrier, such as a pharmaceuticallyacceptable carrier. Since the polypeptides and polynucleotides may bebroken down in the stomach, each is preferably administeredparenterally, including, for example, administration that issubcutaneous, intramuscular, intravenous, or intradermal. Formulationssuitable for parenteral administration include aqueous and non-aqueoussterile injection solutions which may contain anti-oxidants, buffers,bacteriostatic compounds and solutes which render the formulationisotonic with the bodily fluid, preferably the blood, of the individual;and aqueous and non-aqueous sterile suspensions which may includesuspending agents or thickening agents. The formulations may bepresented in unit-dose or multi-dose containers, for example, sealedampoules and vials and may be stored in a freeze-dried conditionrequiring only the addition of the sterile liquid carrier immediatelyprior to use.

The vaccine formulation of the invention may also include adjuvantsystems for enhancing the immunogenicity of the formulation. Preferablythe adjuvant system raises preferentially a TH1 type of response.

An immune response may be broadly distinguished into two extremecategories, being a humoral or cell mediated immune responses(traditionally characterised by antibody and cellular effectormechanisms of protection respectively). These categories of responsehave been termed TH1-type responses (cell-mediated response), andTH2-type immune responses (humoral response).

Extreme TH1-type immune responses may be characterised by the generationof antigen specific, haplotype restricted cytotoxic T lymphocytes, andnatural killer cell responses. In mice TH1-type responses are oftencharacterised by the generation of antibodies of the IgG2a subtype,whilst in the human these correspond to IgG1 type antibodies. TH2-typeimmune responses are characterised by the generation of a broad range ofimmunoglobulin isotypes including in mice IgG1, IgA, and IgM.

It can be considered that the driving force behind the development ofthese two types of immune responses are cytokines. High levels ofTH1-type cytokines tend to favour the induction of cell mediated immuneresponses to the given antigen, whilst high levels of TH2-type cytokinestend to favour the induction of humoral immune responses to the antigen.

The distinction of TH1 and TH2-type immune responses is not absolute. Inreality an individual will support an immune response which is describedas being predominantly TH1 or predominantly TH2. However, it is oftenconvenient to consider the families of cytokines in terms of thatdescribed in murine CD4 +ve T cell clones by Mosmann and Coffman(Mosmann, T. R. and Coffman, R. L. (1989) TH1 and TH2 cells: differentpatterns of lymphokine secretion lead to different functionalproperties. Annual Review of Immunology, 7, p 145-173). Traditionally,TH1-type responses are associated with the production of the INF-γ andIL-2 cytokines by T-lymphocytes. Other cytokines often directlyassociated with the induction of TH1-type immune responses are notproduced by T-cells, such as IL-12. In contrast, TH2-type responses areassociated with the secretion of IL-4, IL-5, IL-6 and IL-13.

It is known that certain vaccine adjuvants are particularly suited tothe stimulation of either TH1 or TH2-type cytokine responses.Traditionally the best indicators of the TH1:TH2 balance of the immuneresponse after a vaccination or infection includes direct measurement ofthe production of TH1 or TH2 cytokines by T lymphocytes in vitro afterrestimulation with antigen, and/or the measurement of the IgG1:IgG2aratio of antigen specific antibody responses.

Thus, a TH1-type adjuvant is one which preferentially stimulatesisolated T-cell populations to produce high levels of TH1-type cytokineswhen re-stimulated with antigen in vitro, and promotes development ofboth CD8+ cytotoxic T lymphocytes and antigen specific immunoglobulinresponses associated with TH1-type isotype.

Adjuvants which are capable of preferential stimulation of the TH1 cellresponse are, described in International Patent Application No. WO94/00153 and WO 95/17209.

3 De-O-acylated monophosphoryl lipid A (3D-MPL) is one such adjuvant.This is known from GB 2220211 (Ribi). Chemically it is a mixture of 3De-O-acylated monophosphoryl lipid A with 4, 5 or 6 acylated chains andis manufactured by Ribi Immunochem, Montana. A preferred form of 3De-O-acylated monophosphoryl lipid A is disclosed in European Patent 0689 454 131 (SmithKline Beecham Biologicals SA).

Preferably, the particles of 3D-MPL are small enough to be sterilefiltered through a 0.22 micron membrane (European Patent number 0 689454).

3D-MPL will be present in the range of 10 μg-100 μg preferably 25-50 μgper dose wherein the antigen will typically be present in a range 2-50μg per dose.

Another preferred adjuvant comprises QS21, an Hplc purified non-toxicfraction derived from the bark of Quillaja Saponaria Molina. Optionallythis may be admixed with 3 De-O-acylated monophosphoryl lipid A(3D-MPL), optionally together with an carrier.

The method of production of QS21 is disclosed in U.S. Pat. No.5,057,540.

Non-reactogenic adjuvant formulations containing QS21 have beendescribed previously (WO 96/33739). Such formulations comprising QS21and cholesterol have been shown to be successful TH1 stimulatingadjuvants when formulated together with an antigen.

Further adjuvants which are preferential stimulators of TH1 cellresponse include immunomodulatory oligonucleotides, for exampleunmethylated CpG sequences as disclosed in WO 96/02555.

Combinations of different TH1 stimulating adjuvants, such as thosementioned hereinabove, are also contemplated as providing an adjuvantwhich is a preferential stimulator of TH1 cell response. For example,QS21 can be formulated together with 3D-MPL. The ratio of QS21: 3D-MPLwill typically be in the order of 1:10 to 10:1; preferably 1:5 to 5:1and often substantially 1:1. The preferred range for optimal synergy is2.5:1 to 1:1 3D-MPL: QS21.

Preferably a carrier is also present in the vaccine compositionaccording to the invention. The carrier may be an oil in water emulsion,or an aluminium salt, such as aluminium phosphate or aluminiumhydroxide.

A preferred oil-in-water emulsion comprises a metabolisible oil, such assqualene, alpha tocopherol and Tween 80. In a particularly preferredaspect the antigens in the vaccine composition according to theinvention are combined with QS21 and 3D-MPL in such an emulsion.Additionally the oil in water emulsion may contain span 85 and/orlecithin and/or tricaprylin.

Typically for human administration QS21 and 3D-MPL will be present in avaccine in the range of 1 μg-200 μg, such as 10-100 μg, preferably 10μg-50 μg per dose. Typically the oil in water will comprise from 2 to10% squalene, from 2 to 10% alpha tocopherol and from 0.3 to 3% tween80. Preferably the ratio of squalene:alpha tocopherol is equal to orless than 1 as this provides a more stable emulsion. Span 85 may also bepresent at a level of 1%. In some cases it may be advantageous that thevaccines of the present invention will further contain a stabiliser.

Non-toxic oil in water emulsions preferably contain a non-toxic oil,e.g. squalane or squalene, an emulsifier, e.g. Tween 80, in an aqueouscarrier. The aqueous carrier may be, for example, phosphate bufferedsaline.

A particularly potent adjuvant formulation involving QS21, 3D-MPL andtocopherol in an oil in water emulsion is described in WO 95/17210.

The present invention also provides a polyvalent vaccine compositioncomprising a vaccine formulation of the invention in combination withother antigens, in particular antigens useful for treating cancers,autoimmune diseases and related conditions. Such a polyvalent vaccinecomposition may include a TH-1 inducing adjuvant as hereinbeforedescribed.

While the invention has been described with reference to certain BASB119polypeptides and polynucleotides, it is to be understood that thiscovers fragments of the naturally occurring polypeptides andpolynucleotides, and similar polypeptides and polynucleotides withadditions, deletions or substitutions which do not substantially affectthe immunogenic properties of the recombinant polypeptides orpolynucleotides.

Compositions, Kits and Administration

In a further aspect of the invention there are provided compositionscomprising a BASB119 polynucleotide and/or a BASB119 polypeptide foradministration to a cell or to a multicellular organism.

The invention also relates to compositions comprising a polynucleotideand/or a polypeptides discussed herein or their agonists or antagonists.The polypeptides and polynucleotides of the invention may be employed incombination with a non-sterile or sterile carrier or carriers for usewith cells, tissues or organisms, such as a pharmaceutical carriersuitable for administration to an individual. Such compositionscomprise, for instance, a media additive or a therapeutically effectiveamount of a polypeptide and/or polynucleotide of the invention and apharmaceutically acceptable carrier or excipient. Such carriers mayinclude, but are not limited to, saline, buffered saline, dextrose,water, glycerol, ethanol and combinations thereof. The formulationshould suit the mode of administration. The invention further relates todiagnostic and pharmaceutical packs and kits comprising one or morecontainers filled with one or more of the ingredients of theaforementioned compositions of the invention.

Polypeptides, polynucleotides and other compounds of the invention maybe employed alone or in conjunction with other compounds, such astherapeutic compounds.

The pharmaceutical compositions may be administered in any effective,convenient manner including, for instance, administration by topical,oral, anal, vaginal, intravenous, intraperitoneal, intramuscular,subcutaneous, intranasal or intradermal routes among others.

In therapy or as a prophylactic, the active agent may be administered toan individual as an injectable composition, for example as a sterileaqueous dispersion, preferably isotonic.

In a further aspect, the present invention provides for pharmaceuticalcompositions comprising a therapeutically effective amount of apolypeptide and/or polynucleotide, such as the soluble form of apolypeptide and/or polynucleotide of the present invention, agonist orantagonist peptide or small molecule compound, in combination with apharmaceutically acceptable carrier or excipient. Such carriers include,but are not limited to, saline, buffered saline, dextrose, water,glycerol, ethanol, and combinations thereof. The invention furtherrelates to pharmaceutical packs and kits comprising one or morecontainers filled with one or more of the ingredients of theaforementioned compositions of the invention. Polypeptides,polynucleotides and other compounds of the present invention may beemployed alone or in conjunction with other compounds, such astherapeutic compounds.

The composition will be adapted to the route of administration, forinstance by a systemic or an oral route. Preferred forms of systemicadministration include injection, typically by intravenous injection.Other injection routes, such as subcutaneous, intramuscular, orintraperitoneal, can be used. Alternative means for systemicadministration include transmucosal and transdermal administration usingpenetrants such as bile salts or fusidic acids or other detergents. Inaddition, if a polypeptide or other compounds of the present inventioncan be formulated in an enteric or an encapsulated formulation, oraladministration may also be possible. Administration of these compoundsmay also be topical and/or localized, in the form of salves, pastes,gels, solutions, powders and the like.

For administration to mammals, and particularly humans, it is expectedthat the daily dosage level of the active agent will be from 0.01 mg/kgto 10 mg/kg, typically around 1 mg/kg. The physician in any event willdetermine the actual dosage which will be most suitable for anindividual and will vary with the age, weight and response of theparticular individual. The above dosages are exemplary of the averagecase. There can, of course, be individual instances where higher orlower dosage ranges are merited, and such are within the scope of thisinvention.

The dosage range required depends on the choice of peptide, the route ofadministration, the nature of the formulation, the nature of thesubject's condition, and the judgment of the attending practitioner.Suitable dosages, however, are in the range of 0.1-100 μg/kg of subject.

A vaccine composition is conveniently in injectable form. Conventionaladjuvants may be employed to enhance the immune response. A suitableunit dose for vaccination is 0.5-5 microgram/kg of antigen, and suchdose is preferably administered 1-3 times and with an interval of 1-3weeks. With the indicated dose range, no adverse toxicological effectswill be observed with the compounds of the invention which wouldpreclude their administration to suitable individuals.

Wide variations in the needed dosage, however, are to be expected inview of the variety of compounds available and the differingefficiencies of various routes of administration. For example, oraladministration would be expected to require higher dosages thanadministration by intravenous injection. Variations in these dosagelevels can be adjusted using standard empirical routines foroptimization, as is well understood in the art.

Sequence Databases, Sequences in a Tangible Medium, and Algorithms

Polynucleotide and polypeptide sequences form a valuable informationresource with which to determine their 2- and 3-dimensional structuresas well as to identify further sequences of similar homology. Theseapproaches are most easily facilitated by storing the sequence in acomputer readable medium and then using the stored data in a knownmacromolecular structure program or to search a sequence database usingwell known searching tools, such as the GCG program package.

Also provided by the invention are methods for the analysis of charactersequences or strings, particularly genetic sequences or encoded proteinsequences. Preferred methods of sequence analysis include, for example,methods of sequence homology analysis, such as identity and similarityanalysis, DNA, RNA and protein structure analysis, sequence assembly,cladistic analysis, sequence motif analysis, open reading framedetermination, nucleic acid base calling, codon usage analysis, nucleicacid base trimming, and sequencing chromatogram peak analysis.

A computer based method is provided for performing homologyidentification. This method comprises the steps of: providing a firstpolynucleotide sequence comprising the sequence of a polynucleotide ofthe invention in a computer readable medium; and comparing said firstpolynucleotide sequence to at least one second polynucleotide orpolypeptide sequence to identify homology.

A computer based method is also provided for performing homologyidentification, said method comprising the steps of: providing a firstpolypeptide sequence comprising the sequence of a polypeptide of theinvention in a computer readable medium; and comparing said firstpolypeptide sequence to at least one second polynucleotide orpolypeptide sequence to identify homology.

All publications and references, including but not limited to patentsand patent applications, cited in this specification are hereinincorporated by reference in their entirety as if each individualpublication or reference were specifically and individually indicated tobe incorporated by reference herein as being fully set forth. Any patentapplication to which this application claims priority is alsoincorporated by reference herein in its entirety in the manner describedabove for publications and references.

DEFINITIONS

“Identity,” as known in the art, is a relationship between two or morepolypeptide sequences or two or more polynucleotide sequences, as thecase may be, as determined by comparing the sequences. In the art,“identity” also means the degree of sequence relatedness betweenpolypeptide or polynucleotide sequences, as the case may be, asdetermined by the match between strings of such sequences. “Identity”can be readily calculated by known methods, including but not limited tothose described in (Computational Molecular Biology, Lesk, A. M., ed.,Oxford University Press, New York, 1988; Biocomputing: Informatics andGenome Projects, Smith, D. W., ed., Academic Press, New York, 1993;Computer Analysis of Sequence Data, Part I, Griffin, A. M., and Griffin,H. G., eds., Humana Press, New Jersey, 1994; Sequence Analysis inMolecular Biology, von Heine, G., Academic Press, 1987; and SequenceAnalysis Primer, Gribskov, M. and Devereux, J., eds., M Stockton Press,New York, 1991; and Carillo, H., and Lipman, D., SIAM J. Applied Math.,48: 1(73 (1988). Methods to determine identity are designed to give thelargest match between the sequences tested. Moreover, methods todetermine identity are codified in publicly available computer programs.Computer program methods to determine identity between two sequencesinclude, but are not limited to, the GAP program in the GCG programpackage (Devereux, J., et al., Nucleic Acids Research 12(1): 387(1984)), BLASTP, BLASTN (Altschul, S. F. et al., J. Molec. Biol. 215:403-410 (1990), and FASTA (Pearson and Lipman Proc. Natl. Acad. Sci. USA85; 2444-2448 (1988). The BLAST family of programs is publicly availablefrom NCBI and other sources (BLAST Manual, Altschul, S., et al., NCBINLM NIH Bethesda, Md. 20894; Altschul, S., et al., J. Mol. Biol. 215:403-410 (1990). The well known Smith Waterman algorithm may also be usedto determine identity.

Parameters for polypeptide sequence comparison include the following:

Algorithm: Needleman and Wunsch, J. Mol. Biol. 48: 443-453 (1970)

Comparison matrix: BLOSSUM62 from Henikoff and Henikoff,

Proc. Natl. Acad. Sci. USA. 89:10915-10919 (1992)

Gap Penalty: 8

Gap Length Penalty: 2

A program useful with these parameters is publicly available as the“gap” program from Genetics Computer Group, Madison Wis. Theaforementioned parameters are the default parameters for peptidecomparisons (along with no penalty for end gaps).

Parameters for polynucleotide comparison include the following:

Algorithm: Needleman and Wunsch, J. Mol Biol. 48: 443-453 (1970)

Comparison matrix: matches=+10, mismatch=0

Gap Penalty: 50

Gap Length Penalty: 3

Available as: The “gap” program from Genetics Computer Group, MadisonWis. These are the default parameters for nucleic acid comparisons.

A preferred meaning for “identity” for polynucleotides and polypeptides,as the case may be, are provided in (1) and (2) below.

(1) Polynucleotide embodiments further include an isolatedpolynucleotide comprising a polynucleotide sequence having at least a50, 60, 70, 80, 85, 90, 95, 97 or 100% identity to the referencesequence of SEQ ID NO:1, wherein said polynucleotide sequence may beidentical to the reference sequence of SEQ ID NO:1 or may include up toa certain integer number of nucleotide alterations as compared to thereference sequence, wherein said alterations are selected from the groupconsisting of at least one nucleotide deletion, substitution, includingtransition and transversion, or insertion, and wherein said alterationsmay occur at the 5′ or 3′ terminal positions of the reference nucleotidesequence or anywhere between those terminal positions, interspersedeither individually among the nucleotides in the reference sequence orin one or more contiguous groups within the reference sequence, andwherein said number of nucleotide alterations is determined bymultiplying the total number of nucleotides in SEQ ID NO:1 by theinteger defining the percent identity divided by 100 and thensubtracting that product from said total number of nucleotides in SEQ IDNO:1, or:

n _(n) ≦x _(n)−(x _(n) ·y),

wherein n_(n) is the number of nucleotide alterations, x_(n) is thetotal number of nucleotides in SEQ ID NO:1, y is 0.50 for 50%, 0.60 for60%, 0.70 for 70%, 0.80 for 80%, 0.85 for 85%, 0.90 for 90%, 0.95 for95%, 0.97 for 97% or 1.00 for 100%, and · is the symbol for themultiplication operator, and wherein any non-integer product of x_(n)and y is rounded down to the nearest integer prior to subtracting itfrom x_(n). Alterations of a polynucleotide sequence encoding thepolypeptide of SEQ ID NO:2 may create nonsense, missense or frameshiftmutations in this coding sequence and thereby alter the polypeptideencoded by the polynucleotide following such alterations.

By way of example, a polynucleotide sequence of the present inventionmay be identical to the reference sequence of SEQ ID NO:1, that is itmay be 100% identical, or it may include up to a certain integer numberof nucleic acid alterations as compared to the reference sequence suchthat the percent identity is less than 100% identity. Such alterationsare selected from the group consisting of at least one nucleic aciddeletion, substitution, including transition and transversion, orinsertion, and wherein said alterations may occur at the 5′ or 3′terminal positions of the reference polynucleotide sequence or anywherebetween those terminal positions, interspersed either individually amongthe nucleic acids in the reference sequence or in one or more contiguousgroups within the reference sequence. The number of nucleic acidalterations for a given percent identity is determined by multiplyingthe total number of nucleic acids in SEQ ID NO:1 by the integer definingthe percent identity divided by 100 and then subtracting that productfrom said total number of nucleic acids in SEQ ID NO:1, or:

n _(n) ≦x _(n)−(x _(n) ·y),

wherein n_(n) is the number of nucleic acid alterations, x_(n) is thetotal number of nucleic acids in SEQ ID NO:1, y is, for instance 0.70for 70%, 0.80 for 80%, 0.85 for 85% etc., · is the symbol for themultiplication operator, and wherein any non-integer product of x_(n)and y is rounded down to the nearest integer prior to subtracting itfrom x_(n).

(2) Polypeptide embodiments further include an isolated polypeptidecomprising a polypeptide having at least a 50, 60, 70, 80, 85, 90, 95,97 or 100% identity to a polypeptide reference sequence of SEQ ID NO:2,wherein said polypeptide sequence may be identical to the referencesequence of SEQ ID NO:2 or may include up to a certain integer number ofamino acid alterations as compared to the reference sequence, whereinsaid alterations are selected from the group consisting of at least oneamino acid deletion, substitution, including conservative andnon-conservative substitution, or insertion, and wherein saidalterations may occur at the amino- or carboxy-terminal positions of thereference polypeptide sequence or anywhere between those terminalpositions, interspersed either individually among the amino acids in thereference sequence or in one or more contiguous groups within thereference sequence, and wherein said number of amino acid alterations isdetermined by multiplying the total number of amino acids in SEQ ID NO:2by the integer defining the percent identity divided by 100 and thensubtracting that product from said total number of amino acids in SEQ IDNO:2, or:

n _(a) ≦x _(a)−(x _(a) ·y),

wherein n_(a) is the number of amino acid alterations, x_(a) is thetotal number of amino acids in SEQ ID NO:2, y is 0.50 for 50%, 0.60 for60%, 0.70 for 70%, 0.80 for 80%, 0.85 for 85%, 0.90 for 90%, 0.95 for95%, 0.97 for 97% or 1.00 for 100%, and · is the symbol for themultiplication operator, and wherein any non-integer product of x_(a)and y is rounded down to the nearest integer prior to subtracting itfrom x_(a).

By way of example, a polypeptide sequence of the present invention maybe identical to the reference sequence of SEQ ID NO:2, that is it may be100% identical, or it may include up to a certain integer number ofamino acid alterations as compared to the reference sequence such thatthe percent identity is less than 100% identity. Such alterations areselected from the group consisting of at least one amino acid deletion,substitution, including conservative and non-conservative substitution,or insertion, and wherein said alterations may occur at the amino- orcarboxy-terminal positions of the reference polypeptide sequence oranywhere between those terminal positions, interspersed eitherindividually among the amino acids in the reference sequence or in oneor more contiguous groups within the reference sequence. The number ofamino acid alterations for a given % identity is determined bymultiplying the total number of amino acids in SEQ ID NO:2 by theinteger defining the percent identity divided by 100 and thensubtracting that product from said total number of amino acids in SEQ IDNO:2, or:

n _(a) ≦x _(a)−(x _(a) ·y),

wherein n_(a) is the number of amino acid alterations, x_(a) is thetotal number of amino acids in SEQ ID NO:2, y is, for instance 0.70 for70%, 0.80 for 80%, 0.85 for 85% etc., and · is the symbol for themultiplication operator, and wherein any non-integer product of x_(a)and y is rounded down to the nearest integer prior to subtracting itfrom x_(a).

“Individual(s),” when used herein with reference to an organism, means amulticellular eukaryote, including, but not limited to a metazoan, amammal, an ovid, a bovid, a simian, a primate, and a human.

“Isolated” means altered “by the hand of man” from its natural state,i.e., if it occurs in nature, it has been changed or removed from itsoriginal environment, or both. For example, a polynucleotide or apolypeptide naturally present in a living organism is not “isolated,”but the same polynucleotide or polypeptide separated from the coexistingmaterials of its natural state is “isolated”, as the term is employedherein. Moreover, a polynucleotide or polypeptide that is introducedinto an organism by transformation, genetic manipulation or by any otherrecombinant method is “isolated” even if it is still present in saidorganism, which organism may be living or non-living.

“Polynucleotide(s)” generally refers to any polyribonucleotide orpolydeoxyribonucleotide, which may be unmodified RNA or DNA or modifiedRNA or DNA including single and double-stranded regions.

“Variant” refers to a polynucleotide or polypeptide that differs from areference polynucleotide or polypeptide, but retains essentialproperties. A typical variant of a polynucleotide differs in nucleotidesequence from another, reference polynucleotide. Changes in thenucleotide sequence of the variant may or may not alter the amino acidsequence of a polypeptide encoded by the reference polynucleotide.Nucleotide changes may result in amino acid substitutions, additions,deletions, fusions and truncations in the polypeptide encoded by thereference sequence, as discussed below. A typical variant of apolypeptide differs in amino acid sequence from another, referencepolypeptide. Generally, differences are limited so that the sequences ofthe reference polypeptide and the variant are closely similar overalland, in many regions, identical. A variant and reference polypeptide maydiffer in amino acid sequence by one or more substitutions, additions,deletions in any combination. A substituted or inserted amino acidresidue may or may not be one encoded by the genetic code. A variant ofa polynucleotide or polypeptide may be a naturally occurring such as anallelic variant, or it may be a variant that is not known to occurnaturally. Non-naturally occurring variants of polynucleotides andpolypeptides may be made by mutagenesis techniques or by directsynthesis.

“Disease(s)” means any disease caused by or related to infection by abacteria, including, for example, otitis media in infants and children,pneumonia in elderlies, sinusitis, nosocomial infections and invasivediseases, chronic otitis media with hearing loss, fluid accumulation inthe middle ear, auditive nerve damage, delayed speech learning,infection of the upper respiratory tract and inflammation of the middleear.

EXAMPLES

The examples below are carried out using standard techniques, which arewell known and routine to those of skill in the art, except whereotherwise described in detail. The examples are illustrative, but do notlimit the invention.

Example 1 DNA Sequencing of the BASB119 Gene from Moraxella catarrhalisStrain ATCC 43617

A: BASB119 in Moraxella catarrhalis Strain.

The BASB119 gene of SEQ ID NO:1 is from Moraxella catarrhalis strainATCC 43617. The translation of the BASB119 polynucleotide sequence isshowed in SEQ ID NO:2.

B: BASB119 in Moraxella Catarrhalis Strain 43617.

The sequence of the BASB119 gene was confirmed in Moraxella Catarrhalisstrain ATCC 43617. For this purpose, plasmid DNA (see example 2A)containing the gene region encoding the mature BASB119 from MoraxellaCatarrhalis. strain ATCC 43617 used as a PCR template. This material wasthen submitted to Polymerase Chain Reaction DNA amplification usingprimers pTLZ F 5′ TGA CAA TTA ATC ATC GGC TCG-3′ [SEQ ID NO:5] andreverse pTLZ RV.2 5′ GGC TGA AAA TCT TCT CTC ATC C-3′ [SEQ ID NO:6]. ThePCR amplicon was then submitted to DNA sequencing using the Big Dyes kit(Applied biosystems) and analyzed on a ABI 373/A DNA sequencer in theconditions described by the supplier. As a result, the polynucleotideand deduced polypeptide sequences, referred to as SEQ ID NO:3 and SEQ IDNO:4 respectively, were obtained. These sequences do not comprise thesignal sequence as the signal sequence was from the plasmid.

Using the MegAlign program from the DNASTAR software package, analignment of the polynucleotide sequences of SEQ ID NO:1 and 3 wasperformed, and is displayed in FIG. 1; a pairwise comparison ofidentities shows that the two BASB119 polynucleotide gene sequences are100% identical in the region coding for the mature protein. Using thesame MegAlign program, an alignment of the polypeptide sequences of SEQID NO:2 and 4 was performed, and is displayed in FIG. 2; a pairwisecomparison of identities shows that the two BASB119 protein sequencesare 100% identical in the region of the mature protein.

Example 2 Construction of Plasmid to Express Recombinant BASB119 A:Cloning of BASB119.

The EcoRI and SalI restriction sites engineered into theMC-Lip11-Fn/t-RI (5′-AGG CAG AGG GAA TTC ATG ATG AGA TTT TTA TTG GTTGG-3′) [SEQ ID NO:7] forward and MC-Lip11RCh/t-Sal (5′-AGG CAG AGG GTCGAC TTA ATG GTG ATG GTG ATG GTG AAA CTG ACT TTC GTC AAT TAT GG-3′) [SEQID NO:8] reverse amplification primers, respectively, permitteddirectional cloning a PCR product into the E. coli expression plasmidpTLZ2 such that a mature BASB119 protein could be expressed as a fusionprotein containing a (His)₆ affinity chromatography tag at theC-terminus. The BASB119 PCR product was purified from the amplificationreaction using silica gel-based spin columns (QiaGen) according to themanufacturers instructions. To produce the required EcoRI and SalItermini necessary for cloning, purified PCR product was sequentiallydigested to completion with EcoRI and SalI restriction enzymes asrecommended by the manufacturer (Life Technologies). Following the firstrestriction digestion, the PCR product was purified via spin column asabove to remove salts and eluted in sterile water prior to the secondenzyme digestion. The digested DNA fragment was again purified usingsilica gel-based spin columns prior to ligation with the pTLZ2 plasmid.

B: Production of Expression Vector.

To prepare the expression plasmid pTLZ2 for ligation, it was similarlydigested to completion with both EcoRI and SalI and then treated withcalf intestinal phosphatase (CIP, ˜0.02 units/pmole of 5′ end, LifeTechnologies) as directed by the manufacturer to prevent self ligation.An approximately 5-fold molar excess of the digested fragment to theprepared vector was used to program the ligation reaction. A standard˜20 μl ligation reaction (˜16° C., ˜16 hours), using methods well knownin the art, was performed using T4 DNA ligase (˜2.0 units/reaction, LifeTechnologies). An aliquot of the ligation (˜5 μl) was used to transformelectro-competent JM109 cells according to methods well known in theart. Following a ˜2-3 hour outgrowth period at 37° C. in ˜1.0 ml of LBbroth, transformed cells were plated on LB agar plates containingampicillin (100 μg/ml). Antibiotic was included in the selection. Plateswere incubated overnight at 37° C. for ˜16 hours. Individual ApRcolonies were picked with sterile toothpicks and used to “patch”inoculate fresh LB ApR plates as well as a ˜1.0 ml LB ApR broth culture.Both the patch plates and the broth culture were incubated overnight at37° C. in either a standard incubator (plates) or a shaking water bath.A whole cell-based PCR analysis was employed to verify thattransformants contained the BASB119 DNA insert. Here, the ˜1.0 mlovernight LB Ap broth culture was transferred to a 1.5 ml polypropylenetube and the cells collected by centrifugation in a Beckmannmicrocentrifuge (˜3 min., room temperature, ˜12,000×g). The cell pelletwas suspended in ˜200 μl of sterile water and a 10?l aliquot used toprogram a ˜50 μl final volume PCR reaction containing both BASB119forward and reverse amplification primers. Final concentrations of thePCR reaction components were essentially the same as those specified inexample 2 except ˜5.0 units of Taq polymerase was used. The initial 95°C. denaturation step was increased to 3 minutes to ensure thermaldisruption of the bacterial cells and liberation of plasmid DNA. An ABIModel 9700 thermal cycler and a 32 cycle, three-step thermalamplification profile, i.e. 95° C., 45 sec; 55-58° C., 45 sec, 72° C., 1min., were used to amplify the BASB119 fragment from the lysedtransformant samples. Following thermal amplification, a ˜20 μl aliquotof the reaction was analyzed by agarose gel electrophoresis (0.8%agarose in a Tris-acetate-EDTA (TAE) buffer). DNA fragments werevisualized by UV illumination after gel electrophoresis and ethidiumbromide staining. A DNA molecular size standard (1 Kb ladder, LifeTechnologies) was electrophoresed in parallel with the test samples andwas used to estimate the size of the PCR products. Transformants thatproduced the expected size PCR product were identified as strainscontaining a BASB119 expression construct. Expression plasmid containingstrains were then analyzed for the inducible expression of recombinantBASB119.

C: Expression Analysis of PCR-Positive Transformants.

For each PCR-positive transformant identified above, ˜5.0 ml of LB brothcontaining ampicillin (100 μg/ml) was inoculated with cells from thepatch plate and grown overnight at 37° C. with shaking (˜250 rpm). Analiquot of the overnight seed culture (˜1.0 ml) was inoculated into a125 ml erlenmeyer flask containing 25 of LB Ap broth and grown at 37° C.with shaking (250 rpm) until the culture turbidity reached O.D.600 of˜0.5, i.e. mid-log phase (usually about 1.5-2.0 hours). At this timeapproximately half of the culture (˜12.5 ml) was transferred to a second125 ml flask and expression of recombinant BASB119 protein induced bythe addition of IPTG (1.0 M stock prepared in sterile water, Sigma) to afinal concentration of 1.0 mM. Incubation of both the IPTG-induced andnon-induced cultures continued for an additional ˜4 hours at 37° C. withshaking. Samples (˜1.0 ml) of both induced and non-induced cultures wereremoved after the induction period and the cells collected bycentrifugation in a microcentrifuge at room temperature for ˜3 minutes.Individual cell pellets were suspended in ˜50 μl of sterile water, thenmixed with an equal volume of 2× Laemelli SDS-PAGE sample buffercontaining 2-mercaptoethanol, and placed in boiling water bath for ˜3min to denature protein. Equal volumes (˜15 μl) of both the crudeIPTG-induced and the non-induced cell lysates were loaded onto duplicate12% Tris/glycine polyacrylamide gel (1 mm thick Mini-gels, Novex). Theinduced and non-induced lysate samples were electrophoresed togetherwith prestained molecular weight markers (SeeBlue, Novex) underconventional conditions using a standard SDS/Tris/glycine running buffer(BioRad). Following electrophoresis, one gel was stained with commassiebrilliant blue R250 (BioRad) and then destained to visualize novelBASB119 IPTG-inducible protein(s). The second gel was electroblottedonto a PVDF membrane (0.45 micron pore size, Novex) for ˜2 hrs at 4° C.using a BioRad Mini-Protean II blotting apparatus and Towbin's methanol(20%) transfer buffer. Blocking of the membrane and antibody incubationswere performed according to methods well known in the art. A monoclonalanti-RGS (His)₃ antibody, followed by a second rabbit anti-mouseantibody conjugated to HRP (QiaGen), was used to confirm the expressionand identity of the BASB119 recombinant protein. Visualization of theanti-His antibody reactive pattern was achieved using either an ABTinsoluble substrate or using Hyperfilm with the Amersham ECLchemiluminescence system.

Example 3 Production of Recombinant BASB119 Bacterial Strain

A recombinant expression strain of E. coli JM109 containing a plasmid(pTLZ2) encoding BASB119 from M. catarrhalis. was used to produce cellmass for purification of recombinant protein. The expression strain wascultivated on LB agar plates containing 100 μg/ml ampicillin (“Ap”) toensure that the pTLZ2 was maintained. For cryopreservation at −80° C.,the strain was propagated in LB broth containing the same concentrationof antibiotics then mixed with an equal volume of LB broth containing30% (w/v) glycerol.

Media

The fermentation medium used for the production of recombinant proteinconsisted of 2×YT broth (Difco) containing 100 μg/ml Ap. Antifoam wasadded to medium for the fermentor at 0.25 ml/L (Antifoam 204, Sigma). Toinduce expression of the BASB119 recombinant protein, IPTG (Isopropylβ-D-Thiogalactopyranoside) was added to the fermentor (1 mM, final).

Fermentation

A 500-ml erlenmeyer seed flask, containing 50 ml working volume, wasinoculated with 0.3 ml of rapidly thawed frozen culture, or severalcolonies from a selective agar plate culture, and incubated forapproximately 12 hours at 37±1° C. on a shaking platform at 150 rpm(Innova 2100, New Brunswick Scientific). This seed culture was then usedto inoculate a 5-L working volume fermentor containing 2×YT broth andboth Ap antibiotics. The fermentor (Bioflo 3000, New BrunswickScientific) was operated at 37±1° C., 0.2-0.4 VVM air sparge, 250 rpm inRushton impellers. The pH was not controlled in either the flask seedculture or the fermentor. During fermentation, the pH ranged 6.5 to 7.3in the fermentor. IPTG (1.0 M stock, prepared in sterile water) wasadded to the fermentor when the culture reached mid-log of growth (˜0.7O.D.600 units). Cells were induced for 2-4 hours then harvested bycentrifugation using either a 28RS Heraeus (Sepatech) or RC5C superspeedcentrifuge (Sorvall Instruments). Cell paste was stored at −20 C untilprocessed.

Chemicals and Materials.

Imidazole and Triton X-100 were purchased from Merck. Aprotinin andTriton X-114 were obtained from Sigma Chemical Company. AEBSF was fromICN-Biochemicals. All other chemicals were reagent grade or better.

Ni-NTA Superflow resin and Penta-His Antibody, BSA free were obtainedfrom QiaGen. MicroBCA assay was obtained from Pierce; Amicon 3 filtersfrom Millipore. Dialysis membrane (MWCO12-14000) were from MFPI, USA.Molecular mass marker (BenchMark ladder) was from Life-technologies.

Example 4 Purification of Recombinant BASB119 from E. coliExtraction—Purification

Cell paste from 500 ml IPTG induced culture (˜4 hours, OD620=0.5) wasresuspended in 40 ml of phosphate buffer pH 7.5 containing 1 mM AEBSFand 1 mM Aprotinin as protease inhibitors. Cells were lysed in a celldisrupter. Lysate was detergent partitioned with 1.5% Triton X-114 for 2hours at 4° C. and centrifuged at 3,000 g for 30 minutes at 4° C.Extract was warmed to 37° C. for 15 minutes and centrifuged at 1,000 gfor 10 minutes at 20° C. Triton phase (lower phase) was diluted up to 15ml with phosphate buffer pH 7.5 containing 0.3M NaCl, 0.005% TritonX-100, 10% glycerol (buffer A) and applied to Ni-NTA superflow resin ina batch mode (overnight incubation). Resin was washed with buffer A.Proteins were eluted with buffer A containing successively 50 mM, 100mM, and 200 mM Imidazole. Fractions containing BASB119 protein werepooled and dialyzed against PBS buffer pH 7.4 containing 0.1% TritonX-100.

Purified BASB119 protein was quantified using Micro BCA assay reagent.

2 mg of purified protein were obtained, at a final concentration of 130μg/ml.

As shown in FIG. 3-A, purified BASB119 protein appeared in SDS-PAGEanalysis as a major band migrating at around 21 kDa (estimated relativemolecular mass). Purity was estimated to more than 80%. BASB119 proteinwas reactive against a mouse monoclonal antibody raised against the6-Histidine, motif (FIG. 3-B).

Example 5 Production of Antisera to Recombinant BASB119

Polyvalent antisera directed against the BASB119 protein were generatedby vaccinating six mice with the purified recombinant BASB119 protein.Each animal is given a total of three immunizations subcutaneously ofabout 10 μg BASB119 protein per injection at approximately 14 daysinterval. Animals were bled prior to the first immunization(“pre-bleed”) and one week after the last immunization.

Anti-BASB119 protein titers were measured by an ELISA using purifiedrecombinant BASB119 protein (4 μg/well). The titre is defined asmid-point titers calculated by 4-parameter logistic model using the XLFit software. The titers obtained post immunisation were 1:1300 for themice sera.

Example 6 Immunological Characterization Surface Exposure of BASB111

Anti-BASB119 protein titers were determined by an ELISA usingformalin-killed whole cells of Moraxella catarrhalis strains 2926 (20μg/well) The titre is defined as mid-point titers calculated by4-parameter logistic model using the SoftMax Pro software.

Titers observed with the rabbit immune sera (1:100) demonstrate that theBASB119 protein is detected at the surface of M. catarrhalis cells.

Example 7 Immunological Characterization Bactericidal Activity

Complement-mediated cytotoxic activity of anti-BASB119 antibodies wasexamined to determine the vaccine potential of BASB119 protein antiserumwas prepared as described above. The activities of the pre-immune serumand the anti-BASB119 antiserum in mediating complement killing of M.catarrhalis were examined.

Strains of M. catarrhalis were grown on Mueller Hinton plates for 24hours at 36° C. Several colonies were added to 15 ml of BHI in the 125ml flask. Cultures were grown for about 4 hours at 200 rpm until theA620=0.4. After one wash step, the pellet was suspended with HBSS andthe strain was diluted to obtain 28500 CFU per milliliter. Fifty (50) μlof preimmune sera and the anti-BASB119 sera (inactivated at 56° C. for30 min) was deposited into the first well of a 96-wells plate and twofold serial dilutions in HBSS were deposited in the other wells of thesame line. Twenty-five (25) μl of live diluted M. catarrhalis wassubsequently added and the mixture was incubated for 15 min at roomtemperature. Baby rabbit complement (Pel freez clinical, systems, BrownDeer, Wis., USA) was added into each well at a working dilution definedbeforehand in a toxicity assay.

Microplates were covered and incubated for 1 hour at 37° C. at 200 rpm.

Each test include a complement control (wells without serum containingactive or inactivated complement source), a positive control (wellscontaining serum with a know titer of bactericidal antibodies), aculture control (wells without serum and complement) and a serum control(wells without complement).

The bactericidal titer of mice antiserum (50% killing of homologousstrain) was <1:25 (pre-immune) and >1:100 (immune).

Example 8 Efficacy of BASB119 Vaccine Enhancement of Lung Clearance ofM. catarrhalis in Mice

This mouse model is based on the analysis of the lung invasion by M.catarrhalis following a standard intranasal challenge to vaccinatedmice.

Groups of 6 BALB/c mice (females, 6 weeks old) are immunizedsubcutaneously with 100 μl of vaccine corresponding to a 10 μg dose andare boosted 2 weeks later. One week after the booster, the mice arechallenged by instillation of 50 μl of bacterial suspension (5 10⁵CFU/50 μl) into the left nostril under anaesthesia (mice areanaesthetised with a combination of ketamine and xylazine anaesthetics,0.24 mg xylazine (Rompun) and 0.8 mg ketamine (Imalgene)/100 μl). Miceare killed 4 hours after challenge and the lungs are removed asepticallyand homogenized individually. The log 10 weighted mean number ofCFU/lung is determined by counting the colonies grown on Mueller-Hintonagar plates after plating of 20 μl of 5 serial dilutions of thehomogenate. The arithmetic mean of the log 10 weighted mean number ofCFU/lung and the standard deviations are calculated for each group.

Results are analysed statistically by applying 1-way ANOVA afterassuming equality of variance (checked by Brown and Forsythe's test) andnormality (checked using the Shapiro-Wilk test). Differences betweengroups were analysed using the Dunnet test, Tukey's studentised rangetest (HSD) and Student-Newman-Keuls test.

In this experiment groups of mice were immunized either with BASB119adsorbed onto AlPO4 (10 ug of BASB119 onto 100 μg of AlPO4) or with akilled whole cells (kwc) preparation of M. catarrhalis strain ATCC 43617adsorbed onto AlPO4 (5 10⁸ cells onto AlPO4) or with 100 μg AlPO4without antigen. The mice were challenged with 5 10⁵ CFU of live M.catarrhalis strain ATCC 43617 bacteria.

The log 10 weighted mean number of CFU/lung and the standard deviation 4hours after challenge were calculated for each group. Sham immunizedmice had 5.41 (+/−0.2) log 10 CFU/lungs 4 hours after challenge

The kwc preparation induced significant lung clearance as compared tothe control group (1.58 log difference). BASB119 vaccine induced a 1.34log difference in lung clearance as compared to the control group, whichwas significantly different from the control.

DEPOSITED MATERIALS

A deposit containing a Moraxella catarrhalis Catlin strain has beendeposited with the American Type Culture Collection (herein “ATCC”) onJun. 21, 1997 and assigned deposit number 43617. The deposit wasdescribed as Branhamella catarrhalis (Frosch and Kolle) and is afreeze-dried, 1.5-2.9 kb insert library constructed from M. catarrhalisisolate obtained from a transtracheal aspirate of a coal miner withchronic bronchitits. The deposit is described in Antimicrob. AgentsChemother. 21: 506-508 (1982).

The Moraxella catarrhalis strain deposit is referred to herein as “thedeposited strain” or as “the DNA of the deposited strain.”

The deposited strain contains a full length BASB119 gene.

A deposit of the vector pMC-D15 consisting of Moraxella catarrhalis DNAinserted in pQE30 has been deposited with the American Type CultureCollection (ATCC) on Feb. 12, 1999 and assigned deposit number 207105.

The sequence of the polynucleotides contained in the depositedstrain/clone, as well as the amino acid sequence of any polypeptideencoded thereby, are controlling in the event of any conflict with anydescription of sequences herein.

The deposit of the deposited strains have been made under the terms ofthe Budapest Treaty on the International Recognition of the Deposit ofMicro-organisms for Purposes of Patent Procedure. The deposited strainswill be irrevocably and without restriction or condition released to thepublic upon the issuance of a patent. The deposited strains are providedmerely as convenience to those of skill in the art and are not anadmission that a deposit is required for enablement, such as thatrequired under 35 U.S.C. §112.

1. An isolated polypeptide comprising an amino acid sequence which hasat least 85% identity to the amino acid sequence selected from the groupconsisting of: SEQ ID NO:2 and SEQ ID NO:4, over the entire length ofSEQ ID NO:2 or SEQ ID NO:4 respectively.
 2. An isolated polypeptide asclaimed in claim 1 in which the amino acid sequence has at least 95%identity to the amino acid sequence selected from the group consistingof: SEQ ID NO:2 and SEQ ID NO:4, over the entire length of SEQ ID NO:2or SEQ ID NO:4 respectively.
 3. The polypeptide as claimed in claim 1comprising the amino acid sequence selected from the group consistingof: SEQ ID NO:2 and SEQ ID NO:4.
 4. An isolated polypeptide of SEQ IDNO:2 or SEQ ID NO:4.
 5. An immunogenic fragment of the polypeptide asclaimed in any one of claims 1 to 4 in which the immunogenic activity ofsaid immunogenic fragment is substantially the same as the polypeptideof SEQ ID NO:2 or SEQ ID NO:4.
 6. A polypeptide as claimed in any ofclaims 1 to 5 wherein said polypeptide is part of a larger fusionprotein.
 7. An isolated polynucleotide encoding a polypeptide as claimedin any of claims 1 to
 6. 8. An isolated polynucleotide comprising anucleotide sequence encoding a polypeptide that has at least 85%identity to the amino acid sequence of SEQ ID NO:2 or 4 over the entirelength of SEQ ID NO:2 or 4 respectively; or a nucleotide sequencecomplementary to said isolated polynucleotide.
 9. An isolatedpolynucleotide comprising a nucleotide sequence that has at least 85%identity to a nucleotide sequence encoding a polypeptide of SEQ ID NO:2or 4 over the entire coding region or a nucleotide sequencecomplementary to said isolated polynucleotide.
 10. An isolatedpolynucleotide which comprises a nucleotide sequence which has at least85% identity to that of SEQ ID NO:1 or 3 over the entire length of SEQID NO:1 or 3 respectively; or a nucleotide sequence complementary tosaid isolated polynucleotide.
 11. The isolated polynucleotide as claimedin any one of claims 7 to 10 in which the identity is at least 95% toSEQ ID NO:1 or
 3. 12. An isolated polynucleotide comprising a nucleotidesequence encoding the polypeptide of SEQ ID NO:2 or SEQ ID NO:4.
 13. Anisolated polynucleotide comprising the polynucleotide of SEQ ID NO:1 orSEQ ID NO:3.
 14. An isolated polynucleotide comprising a nucleotidesequence encoding the polypeptide of SEQ ID NO:2, SEQ ID NO:4 obtainableby screening an appropriate library under stringent hybridizationconditions with a labeled probe having the sequence of SEQ ID NO:1 orSEQ ID NO:3 or a fragment thereof.
 15. An expression vector or arecombinant live microorganism comprising an isolated polynucleotideaccording to any one of claims 7-14.
 16. A host cell comprising theexpression vector of claim 15 or a subcellular fraction or a membrane ofsaid host cell expressing an isolated polypeptide comprising an aminoacid sequence that has at least 85% identity to the amino acid sequenceselected from the group consisting of: SEQ ID NO:2 and SEQ ID NO:4. 17.A process for producing a polypeptide of claims 1 to 6 comprisingculturing a host cell of claim 16 under conditions sufficient for theproduction of said polypeptide and recovering the polypeptide from theculture medium.
 18. A process for expressing a polynucleotide of any oneof claims 7-14 comprising transforming a host cell with the expressionvector comprising at least one of said polynucleotides and culturingsaid host cell under conditions sufficient for expression of any one ofsaid polynucleotides.
 19. A vaccine composition comprising an effectiveamount of the polypeptide of any one of claims 1 to 6 and apharmaceutically acceptable carrier.
 20. A vaccine compositioncomprising an effective amount of the polynucleotide of any one ofclaims 7 to 14 and a pharmaceutically effective carrier.
 21. The vaccinecomposition according to either one of claims 19 or 20 wherein saidcomposition comprises at least one other Moraxella catarrhalis antigen.22. An antibody immunospecific for the polypeptide or immunologicalfragment as claimed in any one of claims 1 to
 6. 23. A method ofdiagnosing a Moraxella catarrhalis infection, comprising identifying apolypeptide as claimed in any one of claims 1-6, or an antibody that isimmunospecific for said polypeptide, present within a biological samplefrom an animal suspected of having such an infection.
 24. Use of acomposition comprising an immunologically effective amount of apolypeptide as claimed in any one of claims 1-6 in the preparation of amedicament for use in generating an immune response in an animal. 25.Use of a composition comprising an immunologically effective amount of apolynucleotide as claimed in any one of claims 7-14 in the preparationof a medicament for use in generating, an immune response in an animal.26. A therapeutic composition useful in treating humans with Moraxellacatarrhalis disease comprising it least one antibody directed againstthe polypeptide of claims 1-6 and a suitable pharmaceutical carrier.